Update upstream source from tag 'upstream/2.3.0+dfsg'
Update to upstream version '2.3.0+dfsg'
with Debian dir ba0e392cc577ac0a5e4a1f511a3f47c1d9abf886
Sascha Steinbiss
4 years ago
0 | EMBL | |
1 | Fasta | |
2 | Genbank | |
3 | Gzipped | |
4 | Kurtz | |
5 | SWISSPROT | |
6 | Vmatch | |
7 | postprocessing | |
8 | pt | |
9 | AtGDB | |
10 | barleypop | |
11 | biophys | |
12 | cDNA | |
13 | dataflow | |
14 | Dataflowfig | |
15 | DJ | |
16 | duesseldorf | |
17 | edu | |
18 | Fernandes | |
19 | Gbp | |
20 | GCB | |
21 | genalyzer | |
22 | GeneChip | |
23 | genomic | |
24 | gif | |
25 | GL | |
26 | html | |
27 | hypa | |
28 | iastate | |
29 | img | |
30 | matchgraph | |
31 | mga | |
32 | oligo | |
33 | patternsearch | |
34 | PatternSearch | |
35 | ||
36 | ||
37 | php | |
38 | PlantGDB | |
39 | possumsearch | |
40 | PossumSearch | |
41 | RescueMu | |
42 | RSA | |
43 | rsat | |
44 | splicenest | |
45 | transposons | |
46 | virtman | |
47 | vmatchlic | |
48 | vmweb | |
49 | vrac | |
50 | Walbot | |
51 | Xenopus | |
52 | zmdb | |
53 | ac | |
54 | AMD | |
55 | Arabidopsis | |
56 | BarleyBase | |
57 | bibiserv | |
58 | bielefeld | |
59 | Bioinformatics | |
60 | biotools | |
61 | cgi | |
62 | commolbio | |
63 | Debian | |
64 | ESTs | |
65 | GenBank | |
66 | hamburg | |
67 | Helden | |
68 | http | |
69 | HyPa | |
70 | KPATH | |
71 | kurtz | |
72 | latexonly | |
73 | mkvtree | |
74 | molgen | |
75 | mpg | |
76 | Multimat | |
77 | oligos | |
78 | org | |
79 | OSX | |
80 | pl | |
81 | plantgdb | |
82 | PowerPC | |
83 | Promide | |
84 | Rahmann | |
85 | Redhat | |
86 | reputer | |
87 | REPuter | |
88 | Sparc | |
89 | SpliceNest | |
90 | src | |
91 | SuSe | |
92 | Sven | |
93 | techfak | |
94 | thaliana | |
95 | ulb | |
96 | vmatch | |
97 | www | |
98 | zbh | |
99 | Zea | |
100 | ASRP | |
101 | GSSanalysis | |
102 | laevis | |
103 | meningioma | |
104 | microarray | |
105 | micromatches | |
106 | miRNA | |
107 | mRNA | |
108 | mutransposon | |
109 | Transposon | |
110 | ABR | |
111 | AKA | |
112 | ALI | |
113 | ALT | |
114 | ALV | |
115 | AME | |
116 | ANG | |
117 | AQU | |
118 | ARN | |
119 | Affymetrix | |
120 | Agave | |
121 | Apr | |
122 | Aureobasidium | |
123 | Azadirachta | |
124 | BAI | |
125 | BAL | |
126 | BEC | |
127 | BEH | |
128 | BEI | |
129 | BEL | |
130 | BER | |
131 | BLA | |
132 | BLI | |
133 | BLO | |
134 | BOD | |
135 | BOH | |
136 | BOR | |
137 | BOU | |
138 | BOV | |
139 | BRE | |
140 | BRI | |
141 | BRO | |
142 | BRU | |
143 | BUC | |
144 | BUE | |
145 | BioExtract | |
146 | Biopieces | |
147 | BlastP | |
148 | CAS | |
149 | CAV | |
150 | CEV | |
151 | CHA | |
152 | CHAU | |
153 | CHE | |
154 | CHI | |
155 | CHO | |
156 | CHOU | |
157 | CHU | |
158 | CLA | |
159 | CLO | |
160 | COH | |
161 | COL | |
162 | CRISPRFinder | |
163 | CRISPRdatabase | |
164 | CRISPRfinder | |
165 | CRISPRs | |
166 | CRO | |
167 | CUL | |
168 | Chlorophyceae | |
169 | Chs | |
170 | CrossLink | |
171 | Cscript | |
172 | CurrentUsage | |
173 | DAR | |
174 | DAS | |
175 | DAV | |
176 | DEA | |
177 | DEE | |
178 | DES | |
179 | DEZ | |
180 | DHA | |
181 | DIBO | |
182 | DIC | |
183 | DIJ | |
184 | DNAVis | |
185 | DOL | |
186 | DOO | |
187 | DOR | |
188 | DUC | |
189 | DUM | |
190 | DUR | |
191 | EBR | |
192 | EIS | |
193 | ELD | |
194 | ELL | |
195 | ENG | |
196 | ERI | |
197 | EST | |
198 | Ecoli | |
199 | FANTOM | |
200 | FAU | |
201 | FER | |
202 | FESCH | |
203 | FIC | |
204 | FIE | |
205 | FLE | |
206 | FOF | |
207 | FOS | |
208 | FRE | |
209 | Floydiella | |
210 | Frankia | |
211 | GAE | |
212 | GAO | |
213 | GAR | |
214 | GAU | |
215 | GEN | |
216 | GEO | |
217 | GER | |
218 | GES | |
219 | GEY | |
220 | GIE | |
221 | GLA | |
222 | GLAE | |
223 | GNF | |
224 | GNI | |
225 | GOL | |
226 | GOM | |
227 | GON | |
228 | GOS | |
229 | GRAE | |
230 | GRE | |
231 | GRI | |
232 | GRO | |
233 | GRU | |
234 | GU | |
235 | GUA | |
236 | Genome | |
237 | GenomeThreader | |
238 | Gepard | |
239 | GmbH | |
240 | Graminella | |
241 | HAA | |
242 | HAB | |
243 | HAC | |
244 | HAK | |
245 | HAN | |
246 | HAR | |
247 | HAU | |
248 | HAZ | |
249 | HEA | |
250 | HED | |
251 | HEL | |
252 | HEP | |
253 | HES | |
254 | HIL | |
255 | HIN | |
256 | HLE | |
257 | HOEH | |
258 | HOF | |
259 | HOL | |
260 | HOM | |
261 | HOR | |
262 | HRI | |
263 | HRV | |
264 | HUL | |
265 | HUR | |
266 | HUS | |
267 | HYS | |
268 | HYT | |
269 | Heliothis | |
270 | IKE | |
271 | IMM | |
272 | Illumina | |
273 | JAC | |
274 | JAI | |
275 | JEN | |
276 | JI | |
277 | JOH | |
278 | JOR | |
279 | JOU | |
280 | KAE | |
281 | KAM | |
282 | KAN | |
283 | KAR | |
284 | KAT | |
285 | KAW | |
286 | KEM | |
287 | KER | |
288 | KEV | |
289 | KHA | |
290 | KLE | |
291 | KNA | |
292 | KOE | |
293 | KOEN | |
294 | KOG | |
295 | KOL | |
296 | KON | |
297 | KOP | |
298 | KOS | |
299 | KOU | |
300 | KOZ | |
301 | KRI | |
302 | KRO | |
303 | KRU | |
304 | KRUE | |
305 | KUB | |
306 | KUC | |
307 | KUD | |
308 | KUG | |
309 | KUM | |
310 | KUR | |
311 | LAL | |
312 | LAM | |
313 | LAR | |
314 | LAU | |
315 | LAZ | |
316 | LBNL | |
317 | LEA | |
318 | LEM | |
319 | LER | |
320 | LI | |
321 | LIA | |
322 | LIN | |
323 | LIU | |
324 | LOEW | |
325 | LOM | |
326 | LOR | |
327 | LScSA | |
328 | LU | |
329 | LUO | |
330 | LUS | |
331 | Leptosira | |
332 | MAA | |
333 | MAL | |
334 | MCC | |
335 | MCL | |
336 | MCM | |
337 | MEH | |
338 | MER | |
339 | MEY | |
340 | MIC | |
341 | MIN | |
342 | MIPSPlantsDB | |
343 | MOC | |
344 | MOE | |
345 | MOH | |
346 | MOL | |
347 | MOR | |
348 | MUL | |
349 | MYE | |
350 | Macronuclear | |
351 | Maize | |
352 | MicroRNAs | |
353 | Mu | |
354 | Myotis | |
355 | NAI | |
356 | NAO | |
357 | NAR | |
358 | NEL | |
359 | NIC | |
360 | NOU | |
361 | NOV | |
362 | NUR | |
363 | NUS | |
364 | NYG | |
365 | Neochloris | |
366 | OHL | |
367 | OKA | |
368 | OSS | |
369 | OTI | |
370 | OTT | |
371 | PAU | |
372 | PAV | |
373 | PEC | |
374 | PEE | |
375 | PEL | |
376 | PFE | |
377 | PLE | |
378 | PLEXdb | |
379 | POB | |
380 | POM | |
381 | POU | |
382 | PRI | |
383 | Piwik | |
384 | PriMUX | |
385 | ProbeMatch | |
386 | QPALMA | |
387 | RAD | |
388 | RAH | |
389 | REE | |
390 | REH | |
391 | REI | |
392 | REN | |
393 | RIN | |
394 | RIS | |
395 | RIV | |
396 | RNA | |
397 | RNAi | |
398 | RNAseq | |
399 | ROS | |
400 | RT | |
401 | RefSeq | |
402 | Rnnotator | |
403 | SAF | |
404 | SAK | |
405 | SAR | |
406 | SCHAA | |
407 | SCHAEF | |
408 | SCHAR | |
409 | SCHAT | |
410 | SCHEL | |
411 | SCHIJ | |
412 | SCHIL | |
413 | SCHLE | |
414 | SCHLU | |
415 | SCHLUE | |
416 | SCHMU | |
417 | SCHNE | |
418 | SCHOE | |
419 | SCHOF | |
420 | SCHOL | |
421 | SCHOO | |
422 | SCHRO | |
423 | SCHUL | |
424 | SCHWA | |
425 | SCHWE | |
426 | SCO | |
427 | SCZ | |
428 | SEG | |
429 | SEI | |
430 | SEK | |
431 | SEV | |
432 | SHA | |
433 | SHI | |
434 | SHU | |
435 | SIE | |
436 | SIM | |
437 | SIMAP | |
438 | SLE | |
439 | SLO | |
440 | SMA | |
441 | SMI | |
442 | SMY | |
443 | SNY | |
444 | SOE | |
445 | SOU | |
446 | SPA | |
447 | SPI | |
448 | STE | |
449 | STEI | |
450 | STEU | |
451 | STO | |
452 | STR | |
453 | STU | |
454 | SU | |
455 | SUL | |
456 | SZY | |
457 | Schwab | |
458 | Seidel | |
459 | Shewanella | |
460 | Silva | |
461 | Slezak | |
462 | Spirodela | |
463 | Stefan | |
464 | Streptococcaceae | |
465 | TAC | |
466 | TAF | |
467 | TAK | |
468 | TAL | |
469 | TAY | |
470 | TEM | |
471 | THA | |
472 | THI | |
473 | TIK | |
474 | TIR | |
475 | TIS | |
476 | TOL | |
477 | TOR | |
478 | TOU | |
479 | TRI | |
480 | TRO | |
481 | TRU | |
482 | TSA | |
483 | TSU | |
484 | TT | |
485 | TUR | |
486 | Tembe | |
487 | Tetrahymena | |
488 | Thellungiella | |
489 | UDE | |
490 | UPA | |
491 | URA | |
492 | UST | |
493 | Univ | |
494 | VAI | |
495 | VAL | |
496 | VAS | |
497 | VAU | |
498 | VEL | |
499 | VER | |
500 | VHA | |
501 | VIN | |
502 | VIT | |
503 | VIV | |
504 | VLA | |
505 | VMatchForArabidopsis | |
506 | VOI | |
507 | VOS | |
508 | VOSS | |
509 | VRA | |
510 | WAL | |
511 | WEI | |
512 | WES | |
513 | WHA | |
514 | WHE | |
515 | WIC | |
516 | WIE | |
517 | WIL | |
518 | WIS | |
519 | WOD | |
520 | WOL | |
521 | WOR | |
522 | WRE | |
523 | WU | |
524 | XU | |
525 | Xanthomonas | |
526 | YAN | |
527 | YU | |
528 | YUN | |
529 | ZAJ | |
530 | ZAL | |
531 | ZAV | |
532 | ZEM | |
533 | ZHA | |
534 | ZHE | |
535 | ZHO | |
536 | ZHU | |
537 | ZIM | |
538 | ZIN | |
539 | aRNH | |
540 | ab | |
541 | al | |
542 | alt | |
543 | articlerender | |
544 | artid | |
545 | biomoby | |
546 | biopieces | |
547 | bp | |
548 | budworm | |
549 | cand | |
550 | chromosomal | |
551 | chromosome | |
552 | chromosomes | |
553 | colorlinks | |
554 | com | |
555 | contigs | |
556 | crispr | |
557 | crosslink | |
558 | daytrial | |
559 | de | |
560 | div | |
561 | dnavis | |
562 | doc | |
563 | enableLinkTracking | |
564 | endophytes | |
565 | epichloid | |
566 | exome | |
567 | exon | |
568 | fcgi | |
569 | fescue | |
570 | fr | |
571 | genmome | |
572 | genome | |
573 | genomes | |
574 | genomethreader | |
575 | getTracker | |
576 | goltsman | |
577 | gov | |
578 | gsf | |
579 | href | |
580 | ht | |
581 | https | |
582 | idsite | |
583 | indels | |
584 | indica | |
585 | informatik | |
586 | interspaced | |
587 | isotigs | |
588 | javascript | |
589 | jgi | |
590 | js | |
591 | li | |
592 | linkcolor | |
593 | llnl | |
594 | lscsa | |
595 | ltr | |
596 | lucifugus | |
597 | mailto | |
598 | maize | |
599 | meliloti | |
600 | mer | |
601 | mers | |
602 | metagenome | |
603 | metagenomes | |
604 | miRNAs | |
605 | microalgae | |
606 | mips | |
607 | mircoRNA | |
608 | mitochondrial | |
609 | ncRNAs | |
610 | nigrifrons | |
611 | nih | |
612 | nl | |
613 | noscript | |
614 | novo | |
615 | oleoabundans | |
616 | oneidensis | |
617 | oryzae | |
618 | parvula | |
619 | pesticidal | |
620 | pigeonpea | |
621 | piwik | |
622 | piwikTracker | |
623 | pkBaseURL | |
624 | plastid | |
625 | polyrhiza | |
626 | preprocess | |
627 | prj | |
628 | probeBase | |
629 | proteome | |
630 | psud | |
631 | pubmedcentral | |
632 | pullulans | |
633 | retroviruses | |
634 | rnafolding | |
635 | seq | |
636 | siRNA | |
637 | simap | |
638 | sp | |
639 | str | |
640 | subfamilies | |
641 | terrestris | |
642 | tex | |
643 | thermophila | |
644 | tigr | |
645 | trackPageView | |
646 | transcriptional | |
647 | transcriptome | |
648 | trialbox | |
649 | tue | |
650 | tuebingen | |
651 | ul | |
652 | unescape | |
653 | uni | |
654 | var | |
655 | virescens | |
656 | weigelworld | |
657 | wiki | |
658 | wmd | |
659 | zenlicensemanager |
0 | \documentclass[11pt]{article} | |
1 | \usepackage{a4wide} | |
2 | \pagestyle{empty} | |
3 | \begin{document} | |
4 | \input{Dataflow.inc} | |
5 | ||
6 | \noindent The dataflow in \emph{Vmatch}. | |
7 | The programs | |
8 | are shown in ellipses. The inputs are the database | |
9 | and the query sequences and the alphabet transformation, | |
10 | represented by rectangles. At the center of all | |
11 | computations the persistent index is shown. All other | |
12 | rectangles represent the different kinds of output. | |
13 | ||
14 | \begin{center} | |
15 | \centerline{\box\graph} | |
16 | \end{center} | |
17 | ||
18 | \end{document} |
0 | vmwebfiles=Dataflowfig.pdf\ | |
1 | AboKurOhl2004.pdf\ | |
2 | AboKurOhl2002.pdf\ | |
3 | BreKurWal2002.pdf\ | |
4 | ChoSchleKurGie2004.pdf\ | |
5 | FitGarKucKurMyeOttSleVitZemMcc2002.pdf\ | |
6 | KurChoOhlSchleStoGie2001.pdf\ | |
7 | HoehKurOhl2002.pdf\ | |
8 | GraeStrKurSte2001.pdf\ | |
9 | BecStroHomGieKur2004.pdf\ | |
10 | KrueSczKurGie2004.pdf\ | |
11 | virtman.pdf | |
12 | ||
13 | PAPERS=${WORK}/archive-etc/own-papers | |
14 | ||
15 | SERVER=vmatchserver | |
16 | WWWBASEDIR=/var/www/html | |
17 | ||
18 | all:vmweb.pdf vmweb.tgz | |
19 | ||
20 | vmweb.pdf:vmweb.tex introduction.inc | |
21 | latexmk vmweb | |
22 | ||
23 | introduction.inc:../virtman.tex introexclude | |
24 | extractpart.pl introduction ../virtman.tex |\ | |
25 | grep -v -f introexclude |\ | |
26 | sed -e 's/\\subsection\*{The parts/\\section*{The parts/' | \ | |
27 | perl -pe 's/\\cite{ABO:KUR:OHL:2004}\.\%\%second/(Abouelhoda, Kurtz, Ohlebusch 2004)./' | \ | |
28 | perl -pe 's/\\cite{(.*)}[\.,]?/\n\\bibentry{\1}\n/' > $@ | |
29 | ||
30 | Dataflow.inc:../Dataflow.pic | |
31 | pic -t ../Dataflow.pic > $@ | |
32 | ||
33 | index.html:vmweb.tex vmweb.pdf introduction.inc replace-header.rb replace-par.rb | |
34 | htlatex vmweb.tex "xhtml, charset=utf-8" " -cunihtf -utf8" | |
35 | cat vmweb.html | replace-header.rb | \ | |
36 | replace-par.rb | \ | |
37 | sed -e 's/CONTENT=/content=/' \ | |
38 | -e 's/ALT=/alt=/' > $@ | |
39 | ||
40 | validate:index.html xhtml-lat1.ent xhtml-symbol.ent xhtml-special.ent xhtml1-transitional.dtd | |
41 | cat index.html | sed -e 's/\"http:\/\/www.w3.org\/TR\/xhtml1\/DTD\//\"/' > .tmp.html | |
42 | xmllint --valid --noout .tmp.html | |
43 | rm -f .tmp.html | |
44 | ||
45 | # also run validation on https://validator.w3.org/ | |
46 | ||
47 | Dataflowfig.dvi:Dataflowfig.tex Dataflow.inc | |
48 | latex Dataflowfig.tex | |
49 | ||
50 | Dataflowfig.pdf:Dataflowfig.dvi | |
51 | dvipdf $< | |
52 | ||
53 | vmweb.tgz:matchgraph.gif ${vmwebfiles} index.html vmweb.pdf | |
54 | tar -cvzf $@ matchgraph.gif ${vmwebfiles} index.html vmweb.pdf | |
55 | ||
56 | virtman.pdf: | |
57 | cp ../virtman.pdf . | |
58 | ||
59 | AboKurOhl2004.pdf: | |
60 | cp ${PAPERS}/$@ . | |
61 | ||
62 | AboKurOhl2002.pdf: | |
63 | cp ${PAPERS}/$@ . | |
64 | ||
65 | BreKurWal2002.pdf: | |
66 | cp ${PAPERS}/$@ . | |
67 | ||
68 | ChoSchleKurGie2004.pdf: | |
69 | cp ${PAPERS}/$@ . | |
70 | ||
71 | FitGarKucKurMyeOttSleVitZemMcc2002.pdf: | |
72 | cp ${PAPERS}/$@ . | |
73 | ||
74 | KurChoOhlSchleStoGie2001.pdf: | |
75 | cp ${PAPERS}/$@ . | |
76 | ||
77 | HoehKurOhl2002.pdf: | |
78 | cp ${PAPERS}/$@ . | |
79 | ||
80 | GraeStrKurSte2001.pdf: | |
81 | cp ${PAPERS}/$@ . | |
82 | ||
83 | KrueSczKurGie2004.pdf: | |
84 | cp ${PAPERS}/$@ . | |
85 | ||
86 | BecStroHomGieKur2004.pdf: | |
87 | cp ${PAPERS}/$@ . | |
88 | ||
89 | installwww: | |
90 | rsync -rv index.html vmweb.css download.html virtman.pdf vmweb.pdf matchgraph.gif distributions $(SERVER):$(WWWBASEDIR) | |
91 | ||
92 | clean: | |
93 | rm -f *.toc *.ilg *.out *.idx *.ind *.dvi *.ps *.log *.aux | |
94 | rm -f *.bbl *.blg | |
95 | rm -f vmweb.4ct vmweb.xref vmweb.tmp vmweb.lg vmweb.idv vmweb.html vmweb.4tc vmweb.fls vmweb.fdb_latexmk | |
96 | rm -f comment.cut introduction.inc | |
97 | rm -f Dataflow.inc | |
98 | rm -f ${vmwebfiles} |
0 | git push kurtz@genometools.org:/home/kurtz/lscsa/vstree.git sk |
0 | <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN" "http://www.w3.org/TR/html4/strict.dtd"> | |
1 | <html> | |
2 | ||
3 | <head> | |
4 | <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1"> | |
5 | <title>Download Vmatch</title> | |
6 | <link rel="stylesheet" type="text/css" href="vmweb.css"> | |
7 | </head> | |
8 | ||
9 | <body> | |
10 | ||
11 | <h1>Download <i>Vmatch</i></h1> | |
12 | ||
13 | <p> | |
14 | By downloading Vmatch you agree to the following: | |
15 | </p> | |
16 | ||
17 | <p> | |
18 | <code> | |
19 | Vmatch is provided on an <strong>AS IS</strong> basis. The developers do not warrant its validity | |
20 | of performance, efficiency, or suitability, nor do they warrant that Vmatch is | |
21 | free from errors. All warranties, including without limitation, any warranty or | |
22 | merchantability or fitness for a particular purpose, are hereby excluded. | |
23 | </code> | |
24 | </p> | |
25 | ||
26 | <h2>Linux</h2> | |
27 | <a href="distributions/vmatch-2.3.0-Linux_x86_64-64bit.tar.gz">vmatch-2.3.0-Linux_x86_64-64bit.tar.gz</a> (2017-06-12)<br/> | |
28 | <a href="distributions/vmatch-2.3.0-Linux_i386-32bit.tar.gz">vmatch-2.3.0-Linux_i386-32bit.tar.gz</a> (2017-06-12)<br/> | |
29 | ||
30 | <h2>Mac OS</h2> | |
31 | <a href="distributions/vmatch-2.3.0-Darwin_i386-64bit.tar.gz">vmatch-2.3.0-Darwin_i386-64bit.tar.gz</a> (2017-06-12)<br/> | |
32 | <a href="distributions/vmatch-2.3.0-Darwin_i386-32bit.tar.gz">vmatch-2.3.0-Darwin_i386-32bit.tar.gz</a> (2017-06-12)<br/> | |
33 | ||
34 | <h2>Windows</h2> | |
35 | <a href="distributions/vmatch-2.3.0-Windows_i686-64bit.zip">vmatch-2.3.0-Windows_i686-64bit.zip</a> (2017-06-12)<br/> | |
36 | <a href="distributions/vmatch-2.3.0-Windows_i686-32bit.zip">vmatch-2.3.0-Windows_i686-32bit.zip</a> (2017-06-12)<br/> | |
37 | ||
38 | <!-- Piwik --> | |
39 | <script type="text/javascript"> | |
40 | var pkBaseURL = "https://zenlicensemanager.com/piwik/"; | |
41 | document.write(unescape("%3Cscript src='" + pkBaseURL + "piwik.js' type='text/javascript'%3E%3C/script%3E")); | |
42 | </script><script type="text/javascript"> | |
43 | try { | |
44 | var piwikTracker = Piwik.getTracker(pkBaseURL + "piwik.php", 3); | |
45 | piwikTracker.trackPageView(); | |
46 | piwikTracker.enableLinkTracking(); | |
47 | } catch( err ) {} | |
48 | </script><noscript><p><img src="https://zenlicensemanager.com/piwik/piwik.php?idsite=3" style="border:0" alt="" /></p></noscript> | |
49 | <!-- End Piwik Tracking Tag --> | |
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51 | </body> | |
52 | </html> |
0 | #!/usr/bin/env perl | |
1 | ||
2 | # select a list of options from a documentation | |
3 | ||
4 | use strict; | |
5 | use warnings; | |
6 | ||
7 | my $numofargs = scalar @ARGV; | |
8 | ||
9 | if($numofargs le 1) | |
10 | { | |
11 | print STDERR "Usage: $0 <tags to be selected> <filename>\n"; | |
12 | exit 1; | |
13 | } | |
14 | ||
15 | my(%tagtab) = (); | |
16 | ||
17 | my $filename = $ARGV[$numofargs-1]; | |
18 | ||
19 | for(my $i=0; $i<$numofargs-1; $i++) | |
20 | { | |
21 | my $key = $ARGV[$i]; | |
22 | $tagtab{$key} = 1; | |
23 | } | |
24 | ||
25 | # Get file data | |
26 | ||
27 | my @filecontents = get_file_data($filename); | |
28 | ||
29 | my $currenttagtext = ''; | |
30 | my $currenttag = ''; | |
31 | my $intag = 0; # inside an option (which can be multiline) | |
32 | ||
33 | for my $line (@filecontents) | |
34 | { | |
35 | if($intag) | |
36 | { | |
37 | if($line =~ /^\%\%\%END{([a-z]+)/) | |
38 | { | |
39 | if($1 ne $currenttag) | |
40 | { | |
41 | print STDERR "$0: BEGIN{$currenttag} ends with END{$1}\n"; | |
42 | exit 1; | |
43 | } | |
44 | print STDERR "\%\%\%matched END with \"$currenttag\"\n"; | |
45 | $intag = 0; | |
46 | print $currenttagtext, "\n"; | |
47 | $currenttagtext = ''; | |
48 | $currenttag = ''; | |
49 | } else | |
50 | { | |
51 | $currenttagtext .= $line; | |
52 | } | |
53 | } else | |
54 | { | |
55 | if($line =~ /^\%\%\%BEGIN{([a-z]+)}/) | |
56 | { | |
57 | print STDERR "\%\%\%matched BEGIN with \"$1\"\n"; | |
58 | if(exists $tagtab{$1}) | |
59 | { | |
60 | $intag = 1; | |
61 | $currenttag = $1; | |
62 | } | |
63 | } | |
64 | } | |
65 | } | |
66 | ||
67 | exit 0; | |
68 | ||
69 | # check if the number of arguments is as expected | |
70 | # get last argument | |
71 | ||
72 | sub get_file_data | |
73 | { | |
74 | my($filename) = @_; | |
75 | ||
76 | unless(open(GET_FILE_DATA, $filename)) | |
77 | { | |
78 | print STDERR "$0: Cannot open file $filename\n"; | |
79 | exit 1; | |
80 | } | |
81 | my @filedata = <GET_FILE_DATA>; | |
82 | close GET_FILE_DATA; | |
83 | return @filedata; | |
84 | } |
0 | <?xml version="1.0" encoding="utf-8" ?> | |
1 | <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" | |
2 | "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> | |
3 | <!--http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd--> | |
4 | <html xmlns="http://www.w3.org/1999/xhtml" | |
5 | > | |
6 | <head><title>The Vmatch large scale sequence analysis software</title> | |
7 | <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> | |
8 | <meta name="generator" content="TeX4ht (http://www.tug.org/tex4ht/)" /> | |
9 | <meta name="originator" content="TeX4ht (http://www.tug.org/tex4ht/)" /> | |
10 | <!-- xhtml,charset=utf-8,html --> | |
11 | <meta name="src" content="vmweb.tex" /> | |
12 | <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1"/> | |
13 | <meta name="description" content="The Vmatch large scale sequence analysis | |
14 | software is a versatile software tool for efficiently solving large scale sequence matching tasks."/> | |
15 | <meta name="keywords" content="sequence analysis, sequence mapping, BLAST, bioinformatics, computational biology"/> | |
16 | <meta http-equiv="Content-Style-Type" content="text/css"/> | |
17 | <link rel="stylesheet" type="text/css" href="vmweb.css" /> | |
18 | </head><body | |
19 | > | |
20 | <div class="maketitle"> | |
21 | ||
22 | ||
23 | ||
24 | ||
25 | ||
26 | ||
27 | ||
28 | <h1 align="center" class="titleHead">The Vmatch large scale sequence analysis | |
29 | software</h1> | |
30 | <div align="center" class="author" ><span | |
31 | class="ptmr7t-x-x-144">Stefan Kurtz</span></div> | |
32 | <br /> | |
33 | <div align="center" class="date" ><span | |
34 | class="ptmr7t-x-x-144">June 15, 2017</span></div> | |
35 | </div> | |
36 | <!--l. 61--> <br/> <center> <img src="matchgraph.gif" alt="show matches of different sizes in a matchgraph"/> </center> <div id="downloadbox"> <ul> <li><a href="download.html">Download <i>Vmatch</i>!</a></li> </ul> </div> | |
37 | <!--l. 63--><p class="noindent" >This is the web-site for <span | |
38 | class="ptmri7t-x-x-120">Vmatch</span>, a versatile software tool for efficiently solving large | |
39 | scale sequence matching tasks. <span | |
40 | class="ptmri7t-x-x-120">Vmatch </span>subsumes the software tool <a | |
41 | href="http://bibiserv.techfak.uni-bielefeld.de/reputer" >REPuter</a>, but is | |
42 | much more general, with a very flexible user interface, and improved space and time | |
43 | requirements. <a href="vmweb.pdf">Here</a> is a printable version of this HTML-page in PDF. | |
44 | </p> | |
45 | <h3 class="likesectionHead"><a | |
46 | id="x1-1000"></a>Features of <span | |
47 | class="ptmri7t-x-x-120">Vmatch</span></h3> | |
48 | <!--l. 76--><p class="noindent" >The <a | |
49 | href="virtman.pdf" ><span | |
50 | class="ptmri7t-x-x-120">Vmatch</span>-manual</a> gives many examples on how to use <span | |
51 | class="ptmri7t-x-x-120">Vmatch</span>. Here are the | |
52 | program’s most important features. | |
53 | </p><!--l. 3--><p class="noindent" > | |
54 | </p> | |
55 | ||
56 | ||
57 | ||
58 | <h4 class="likesubsectionHead"><a | |
59 | id="x1-2000"></a>Persistent index</h4> | |
60 | <!--l. 4--><p class="noindent" >Usually, in a large scale matching problem, extensive portions of the sequences under | |
61 | consideration are static, i.e. they do not change much over time. Therefore it makes | |
62 | sense to preprocess this static data to extract information from it and to store this in a | |
63 | structured manner, allowing efficient searches. <span | |
64 | class="ptmri7t-x-x-120">Vmatch </span>does exactly this: it | |
65 | preprocesses a set of sequences into an index structure. This is stored as a collection of | |
66 | several files constituting the persistent index. The index efficiently represents all | |
67 | substrings of the preprocessed sequences and, unlike many other sequence | |
68 | comparison tools, allows matching tasks to be solved in time, <span | |
69 | class="ptmri7t-x-x-120">independent </span>of | |
70 | the size of the index. Different matching tasks require different parts of the | |
71 | index, but only the required parts of the index are accessed during the matching | |
72 | process. | |
73 | </p><!--l. 21--><p class="noindent" > | |
74 | </p> | |
75 | <h4 class="likesubsectionHead"><a | |
76 | id="x1-3000"></a>Alphabet independency</h4> | |
77 | <!--l. 22--><p class="noindent" >Most software tools for sequence analysis are restricted to DNA and/or protein | |
78 | sequences. In contrast, <span | |
79 | class="ptmri7t-x-x-120">Vmatch </span>can process sequences over any user defined alphabet | |
80 | not larger than 250 symbols. <span | |
81 | class="ptmri7t-x-x-120">Vmatch </span>fully implements the concept of <span | |
82 | class="ptmri7t-x-x-120">symbol</span> | |
83 | <span | |
84 | class="ptmri7t-x-x-120">mappings</span>, denoting alphabet transformations. These allow the user to specify that | |
85 | different characters in the input sequences should be considered identical in | |
86 | the matching process. This feature is used to group similar amino acids, for | |
87 | example. | |
88 | </p><!--l. 31--><p class="noindent" > | |
89 | </p> | |
90 | <h4 class="likesubsectionHead"><a | |
91 | id="x1-4000"></a>Versatility</h4> | |
92 | <!--l. 32--><p class="noindent" ><span | |
93 | class="ptmri7t-x-x-120">Vmatch </span>allows a multitude of different matching tasks to be solved using the | |
94 | persistent index. Every matching task is basically characterized by (1) the <span | |
95 | class="ptmri7t-x-x-120">kind</span> | |
96 | <span | |
97 | class="ptmri7t-x-x-120">of sequences </span>to be matched, (2) the <span | |
98 | class="ptmri7t-x-x-120">kind of matches </span>sought, (3) additional | |
99 | <span | |
100 | class="ptmri7t-x-x-120">constraints </span>on the matches, and (4) the <span | |
101 | class="ptmri7t-x-x-120">kind of postprocessing </span>to be done with the | |
102 | matches. | |
103 | ||
104 | ||
105 | ||
106 | </p><!--l. 39--><p class="noindent" >In the standard case, <span | |
107 | class="ptmri7t-x-x-120">Vmatch </span>matches sequences over the same alphabet. Additionally, | |
108 | DNA sequences can be matched against a protein sequence index in all six reading | |
109 | frames. Finally, DNA sequences can be transformed in all six reading frames and | |
110 | compared against itself. | |
111 | </p><!--l. 44--><p class="noindent" >Where appropriate, <span | |
112 | class="ptmri7t-x-x-120">Vmatch </span>can compute the following kinds of matches, using | |
113 | state-of-the-art algorithms: | |
114 | </p> | |
115 | <ul class="itemize1"> | |
116 | <li class="itemize">maximal and supermaximal repeats using the algorithms of <a | |
117 | id="XABO:KUR:OHL:2004"></a>M.I. | |
118 | Abouelhoda, S. Kurtz, and E. Ohlebusch. Replacing suffix trees with | |
119 | enhanced suffix arrays. <span | |
120 | class="ptmri7t-x-x-120">Journal of Discrete Algorithms</span>, 2:53–86, 2004 | |
121 | </li> | |
122 | <li class="itemize">branching tandem repeats using the algorithm of <a | |
123 | id="XABO:KUR:OHL:2002"></a>M.I. Abouelhoda, | |
124 | S. Kurtz, and E. Ohlebusch. The enhanced suffix array and its applications | |
125 | to genome analysis. In <span | |
126 | class="ptmri7t-x-x-120">Proceedings of the Second Workshop on Algorithms</span> | |
127 | <span | |
128 | class="ptmri7t-x-x-120">in Bioinformatics</span>, pages 449–463. Lecture Notes in Computer Science | |
129 | 2452, Springer-Verlag, 2002 | |
130 | </li> | |
131 | <li class="itemize">maximal (unique) substring matches using the algorithms of <a | |
132 | id="XKUR:2002B"></a>S. Kurtz. A | |
133 | Time and Space Efficient Algorithm for the Substring Matching Problem, | |
134 | 2002 | |
135 | </li> | |
136 | <li class="itemize">complete matches using the algorithms of <a | |
137 | id="XMAN:MYE:1993"></a>U. Manber and E.W. Myers. | |
138 | Suffix Arrays: A New Method for On-Line String Searches. <span | |
139 | class="ptmri7t-x-x-120">SIAM Journal</span> | |
140 | <span | |
141 | class="ptmri7t-x-x-120">on Computing</span>, 22(5):935–948, 1993 and [<a | |
142 | href="#XMYE:1999">86</a>] | |
143 | </li></ul> | |
144 | <!--l. 69--><p class="noindent" >To compute degenerate substring matches or degenerate repeats, each kind | |
145 | of match (with the exception of tandem repeats and complete matches) can | |
146 | be taken as an exact seed and extended by either of two different strategies: | |
147 | </p> | |
148 | <ul class="itemize1"> | |
149 | <li class="itemize">the <span | |
150 | class="ptmri7t-x-x-120">maximum error </span>extension strategy, as described in | |
151 | ||
152 | ||
153 | ||
154 | <!--l. 77--><p class="noindent" ><a | |
155 | id="XKUR:CHO:OHL:SCHLE:STO:GIE:2001"></a>S. Kurtz, J.V. Choudhuri, E. Ohlebusch, C. Schleiermacher, J. Stoye, and | |
156 | R. Giegerich. REPuter: The manifold applications of repeat analysis on | |
157 | a genomic scale. <span | |
158 | class="ptmri7t-x-x-120">Nucleic Acids Res.</span>, 29(22):4633–4642, 2001 for repeat | |
159 | detection, | |
160 | </p></li> | |
161 | <li class="itemize">the <span | |
162 | class="ptmri7t-x-x-120">greedy </span>extension strategy of <a | |
163 | id="XZHA:SCHWA:WAG:MIL:2000"></a>Z. Zhang, S. Schwartz, L. Wagner, | |
164 | and W. Miller. A Greedy Algorithm for Aligning DNA Sequences. | |
165 | <span | |
166 | class="ptmri7t-x-x-120">J.</span><span | |
167 | class="ptmri7t-x-x-120"> Comp.</span><span | |
168 | class="ptmri7t-x-x-120"> Biol.</span>, 7(1/2):203–214, 2000 | |
169 | </li></ul> | |
170 | <!--l. 84--><p class="noindent" >Matches can be selected according to their length, their E-value, their identity value, or | |
171 | match score. | |
172 | </p><!--l. 87--><p class="noindent" >In the standard case, a match is displayed as an alignment including positional | |
173 | information. Alternatively, a match can directly be postprocessed in different | |
174 | ways: | |
175 | </p> | |
176 | <ul class="itemize1"> | |
177 | <li class="itemize"><span | |
178 | class="ptmri7t-x-x-120">inverse output</span>, i.e. reporting of substrings <span | |
179 | class="ptmri7t-x-x-120">not </span>covered by a match. | |
180 | </li> | |
181 | <li class="itemize"><span | |
182 | class="ptmri7t-x-x-120">masking </span>of substrings covered by a match. | |
183 | </li> | |
184 | <li class="itemize"><span | |
185 | class="ptmri7t-x-x-120">clustering </span>of sequences according to the matches found. | |
186 | </li> | |
187 | <li class="itemize"><span | |
188 | class="ptmri7t-x-x-120">chaining </span>of matches, i.e. finding optimal subsets of matches which do not | |
189 | cross, using the algorithms described in | |
190 | <!--l. 104--><p class="noindent" ><a | |
191 | id="XABO:OHL:2003"></a>M.I. Abouelhoda and E. Ohlebusch. A Local Chaining Algorithm | |
192 | and its Applications in Comparative Genomics. In <span | |
193 | class="ptmri7t-x-x-120">Proc. 3rd Worksh.</span> | |
194 | <span | |
195 | class="ptmri7t-x-x-120">Algorithms in Bioinformatics (WABI 2003)</span>, number 2812 in Lecture Notes | |
196 | in Bioinformatics, pages 1–16. Springer-Verlag, 2003 | |
197 | </p></li> | |
198 | <li class="itemize"><span | |
199 | class="ptmri7t-x-x-120">clustering </span>of matches according to pairwise sequence similarities computed | |
200 | ||
201 | ||
202 | ||
203 | by the dynamic programming algorithm of <a | |
204 | id="XUKK:1985A"></a>E. Ukkonen. Algorithms for | |
205 | Approximate String Matching. <span | |
206 | class="ptmri7t-x-x-120">Information and Control</span>, 64:100–118, 1985 | |
207 | </li> | |
208 | <li class="itemize"><span | |
209 | class="ptmri7t-x-x-120">clustering </span>of matches according to the positions where they occur, following | |
210 | the approach of | |
211 | <!--l. 115--><p class="noindent" ><a | |
212 | id="XVOL:HAA:SAL:2001"></a>N. Volfovsky, | |
213 | B.J. Haas, and S.L. Salzberg. A Clustering Method for Repeat Analysis in | |
214 | DNA Sequences. <span | |
215 | class="ptmri7t-x-x-120">Genome Biology</span>, 2(8):research0027.1–0027.11, 2001 | |
216 | </p> | |
217 | </li></ul> | |
218 | <!--l. 119--><p class="noindent" > | |
219 | </p> | |
220 | <h4 class="likesubsectionHead"><a | |
221 | id="x1-5000"></a>Efficient algorithms and data structures</h4> | |
222 | <!--l. 120--><p class="noindent" ><span | |
223 | class="ptmri7t-x-x-120">Vmatch </span>is based on enhanced suffix arrays described Abouelhoda, Kurtz & Ohlebusch, | |
224 | 2004. This data structure has been shown to be as powerful as suffix trees, with the | |
225 | advantage of a reduced space requirement and reduced processing time. Careful | |
226 | implementation of the algorithms and data structures incorporated in <span | |
227 | class="ptmri7t-x-x-120">Vmatch</span> | |
228 | have led to exceedingly fast and robust software, allowing very large sequence | |
229 | sets to be processed quickly. The 32-bit version of <span | |
230 | class="ptmri7t-x-x-120">Vmatch </span>can process up to | |
231 | 400 million symbols, if enough memory is available. For large server class | |
232 | machines (e.g. SUN-Sparc/Solaris, Intel Xeon/Linux, Compaq-Alpha/Tru64) | |
233 | <span | |
234 | class="ptmri7t-x-x-120">Vmatch </span>is available as a 64 bit version, enabling gigabytes of sequences to be | |
235 | processed. | |
236 | </p><!--l. 138--><p class="noindent" > | |
237 | </p> | |
238 | <h4 class="likesubsectionHead"><a | |
239 | id="x1-6000"></a>Flexible input format</h4> | |
240 | <!--l. 139--><p class="noindent" >The most common formats for input sequences (Fasta, Genbank, EMBL, and | |
241 | SWISSPROT) are accepted. The user does not have to specify the input format. It is | |
242 | ||
243 | ||
244 | ||
245 | automatically recognized. All input files can contain an arbitrary number of sequences. | |
246 | Gzipped compressed inputs are accepted. | |
247 | </p><!--l. 145--><p class="noindent" > | |
248 | </p> | |
249 | <h4 class="likesubsectionHead"><a | |
250 | id="x1-7000"></a>Customized output and match selection</h4> | |
251 | <!--l. 146--><p class="noindent" ><span | |
252 | class="ptmri7t-x-x-120">Vmatch</span>’s output can be parsed by other programs easily. Furthermore, several options | |
253 | allow for its customization. XML output is available and new output formats can easily | |
254 | be incorporated without changing <span | |
255 | class="ptmri7t-x-x-120">Vmatch</span>’s program code. Certain matches can easily | |
256 | be selected by user defined criteria, without intermediate output and subsequent | |
257 | parsing. | |
258 | </p><!--l. 154--><p class="noindent" > | |
259 | </p> | |
260 | <h3 class="likesectionHead"><a | |
261 | id="x1-8000"></a>The parts of Vmatch</h3> | |
262 | <!--l. 155--><p class="noindent" >Up until now we have referred to <span | |
263 | class="ptmri7t-x-x-120">Vmatch </span>as a collection of programs. In the following | |
264 | we use the same name, <span | |
265 | class="cmtt-12">vmatch </span>(in typewriter font), for the most important | |
266 | program in this collection. Besides <span | |
267 | class="cmtt-12">vmatch</span>, there are the following programs | |
268 | available: | |
269 | </p><ol class="enumerate1" > | |
270 | <li | |
271 | class="enumerate" id="x1-8002x1"><span | |
272 | class="cmtt-12">mkvtree </span>constructs the persistent index and stores it on files. | |
273 | </li> | |
274 | <li | |
275 | class="enumerate" id="x1-8004x2"><span | |
276 | class="cmtt-12">mkdna6idx </span>constructs an index for a DNA sequence after translating this in | |
277 | all six reading frames. | |
278 | </li> | |
279 | <li | |
280 | class="enumerate" id="x1-8006x3"><span | |
281 | class="cmtt-12">vseqinfo </span>delivers information about indexed database sequences. | |
282 | </li> | |
283 | <li | |
284 | class="enumerate" id="x1-8008x4"><span | |
285 | class="cmtt-12">vstree2tex </span>outputs a representation of the index in <span class="LATEX">L<span class="A">A</span><span class="TEX">T<span | |
286 | class="E">E</span>X</span></span>-format. It can | |
287 | be used, for example, for educational or debugging purposes. | |
288 | ||
289 | ||
290 | ||
291 | </li> | |
292 | <li | |
293 | class="enumerate" id="x1-8010x5"><span | |
294 | class="cmtt-12">vseqselect </span>selects indexed sequences satisfying specific criteria. | |
295 | </li> | |
296 | <li | |
297 | class="enumerate" id="x1-8012x6"><span | |
298 | class="cmtt-12">vsubseqselect </span>selects substrings of a specified length range from an | |
299 | index. | |
300 | </li> | |
301 | <li | |
302 | class="enumerate" id="x1-8014x7"><span | |
303 | class="cmtt-12">vmigrate.sh </span>converts an index from big endian to little endian | |
304 | architectures, or vice versa. | |
305 | </li> | |
306 | <li | |
307 | class="enumerate" id="x1-8016x8"><span | |
308 | class="cmtt-12">vmatchselect </span>sort and selects matches delivered by <span | |
309 | class="cmtt-12">vmatch</span>. | |
310 | </li> | |
311 | <li | |
312 | class="enumerate" id="x1-8018x9"><span | |
313 | class="cmtt-12">chain2dim </span>computes optimal chains of matches from files in | |
314 | <span | |
315 | class="ptmri7t-x-x-120">Vmatch</span>-format. | |
316 | </li> | |
317 | <li | |
318 | class="enumerate" id="x1-8020x10"><span | |
319 | class="cmtt-12">matchcluster </span>computes clusters of matches from files in <span | |
320 | class="ptmri7t-x-x-120">Vmatch</span>-format.</li></ol> | |
321 | <!--l. 85--><p class="noindent" > <a href="Dataflowfig.pdf">Here</a> is an overview of the dataflow in <i>Vmatch</i>. | |
322 | </p><!--l. 87--><p class="noindent" > | |
323 | </p> | |
324 | <h3 class="likesectionHead"><a | |
325 | id="x1-9000"></a>Related tools</h3> | |
326 | <!--l. 88--><p class="noindent" >There are several tools which are based on the persistent index of <span | |
327 | class="ptmri7t-x-x-120">Vmatch</span>: | |
328 | </p><!--l. 91--><p class="noindent" > | |
329 | </p><dl class="description"><dt class="description"> | |
330 | <span | |
331 | class="ptmb7t-x-x-120">Genalyzer</span> </dt><dd | |
332 | class="description">is a graphical user interface to visualize the output of <span | |
333 | class="ptmri7t-x-x-120">Vmatch </span>in form | |
334 | of a match graph. For details see | |
335 | <!--l. 97--><p class="noindent" ><a | |
336 | id="XCHO:SCHLE:KUR:GIE:2004"></a>J.V. Choudhuri, C. Schleiermacher, S. Kurtz, and R. Giegerich. | |
337 | Genalyzer: Interactive visualization of sequence similarities between entire | |
338 | genomes. <span | |
339 | class="ptmri7t-x-x-120">Bioinformatics</span>, 20:1964–1965, 2004 | |
340 | </p><!--l. 99--><p class="noindent" >Genalyzer is not available any more. | |
341 | ||
342 | ||
343 | ||
344 | </p></dd><dt class="description"> | |
345 | <a | |
346 | href="http://bibiserv.techfak.uni-bielefeld.de/mga/" ><span | |
347 | class="ptmb7t-x-x-120">MGA</span></a> </dt><dd | |
348 | class="description">is a program to compute multiple alignments of complete genomes. For | |
349 | details see | |
350 | <!--l. 104--><p class="noindent" ><a | |
351 | id="XHOEH:KUR:OHL:2002"></a>M. Höhl, S. Kurtz, and E. Ohlebusch. Efficient multiple genome | |
352 | alignment. <span | |
353 | class="ptmri7t-x-x-120">Bioinformatics</span>, 18(Suppl. 1):S312–S320, 2002 | |
354 | </p></dd><dt class="description"> | |
355 | <span | |
356 | class="ptmb7t-x-x-120">Multimat</span> </dt><dd | |
357 | class="description">is a program to compute multiple exact matches between three or more | |
358 | genome size sequences. For details see | |
359 | <!--l. 108--><p class="noindent" ><a | |
360 | id="XOHL:KUR:2008"></a>E. Ohlebusch and S. Kurtz. Space efficient computation of rare | |
361 | maximal exact matches between multiple sequences. <span | |
362 | class="ptmri7t-x-x-120">J.</span><span | |
363 | class="ptmri7t-x-x-120"> Comp.</span><span | |
364 | class="ptmri7t-x-x-120"> Biol.</span>, | |
365 | 15(4):357–377, 2008 | |
366 | </p><!--l. 110--><p class="noindent" >Please contact <a | |
367 | href="http://www.zbh.uni-hamburg.de/kurtz" >Stefan Kurtz</a> if you are interested in using Multimat. | |
368 | </p></dd><dt class="description"> | |
369 | <a | |
370 | href="http://bibiserv.techfak.uni-bielefeld.de/possumsearch/" ><span | |
371 | class="ptmb7t-x-x-120">PossumSearch</span></a> </dt><dd | |
372 | class="description">Is a program to search for position specific scoring matrices. For | |
373 | details, see | |
374 | <!--l. 118--><p class="noindent" ><a | |
375 | id="XBEC:HOM:GIE:KUR:2006"></a>M. Beckstette, R. Homann, R. Giegerich, and S. Kurtz. Fast index based | |
376 | algorithms and software for matching position specific scoring matrices. | |
377 | <span | |
378 | class="ptmri7t-x-x-120">BMC Bioinformatics</span>, 7:389, 2006 | |
379 | </p></dd><dt class="description"> | |
380 | </dt><dd | |
381 | class="description"> | |
382 | </dd><dt class="description"> | |
383 | <a | |
384 | href="http://www.genomethreader.org/" ><span | |
385 | class="ptmb7t-x-x-120">GenomeThreader</span></a> </dt><dd | |
386 | class="description">is a software tool to compute gene structure predictions. The | |
387 | gene structure predictions are calculated using a similarity-based approach | |
388 | where additional cDNA/EST and/or protein sequences are used to predict | |
389 | gene structures via spliced alignments. <span | |
390 | class="ptmri7t-x-x-120">GenomeThreader </span>uses the matching | |
391 | capabilities of <span | |
392 | class="ptmri7t-x-x-120">Vmatch </span>to efficiently map the reference sequence to a | |
393 | genomic sequence. For details, see | |
394 | <!--l. 128--><p class="noindent" ><a | |
395 | id="XGRE:BRE:SPA:KUR:2005"></a>G. Gremme, V. Brendel, M.E. Sparks, and S. Kurtz. Engineering a | |
396 | software tool for gene prediction in higher organisms. <span | |
397 | class="ptmri7t-x-x-120">Information and</span> | |
398 | <span | |
399 | class="ptmri7t-x-x-120">Software Technology</span>, 47(15):965–978, 2005 | |
400 | </p></dd><dt class="description"> | |
401 | </dt><dd | |
402 | class="description"> | |
403 | ||
404 | ||
405 | ||
406 | </dd><dt class="description"> | |
407 | <a | |
408 | href="http://www.biopieces.org/" ><span | |
409 | class="ptmb7t-x-x-120">Biopieces</span></a> </dt><dd | |
410 | class="description">is a collection of bioinformatics tools that can be pieced together | |
411 | in a very easy and flexible manner to perform both simple and | |
412 | complex tasks. Some Biopieces depend on <span | |
413 | class="ptmri7t-x-x-120">Vmatch</span>. For details see | |
414 | <a | |
415 | href="http://www.biopieces.org/" class="url" ><span | |
416 | class="cmtt-12">http://www.biopieces.org/</span></a>.</dd></dl> | |
417 | <!--l. 139--><p class="noindent" > <a name="CurrentUsage"/> | |
418 | </p> | |
419 | <h3 class="likesectionHead"><a | |
420 | id="x1-10000"></a>Previous and Current Usages</h3> | |
421 | <!--l. 142--><p class="noindent" >We provide an annotated bibliography listing papers which applied <span | |
422 | class="ptmri7t-x-x-120">Vmatch </span>and shortly | |
423 | describe the tasks for which <span | |
424 | class="ptmri7t-x-x-120">Vmatch </span>was used. We omit our own papers. The references | |
425 | were collected by a <a | |
426 | href="https://scholar.google.de/scholar?q=Vmatch+AND+Kurtz+OR+www.vmatch.de" >search in Google scholar</a> (which, as of Jan 2, 2016 retrieved 397 | |
427 | results.) | |
428 | </p><!--l. 149--><p class="noindent" > | |
429 | </p> | |
430 | <h4 class="likesubsectionHead"><a | |
431 | id="x1-11000"></a>Usages in Plant Genome Research</h4> | |
432 | <!--l. 150--><p class="noindent" > | |
433 | </p><ol class="enumerate1" > | |
434 | <li | |
435 | class="enumerate" id="x1-11002x1"><a | |
436 | id="XBRE:KUR:WAL:2002"></a>V. Brendel, S. Kurtz, and V. Walbot. Comparative genomics of | |
437 | Arabidopsis and Maize: Prospects and limitations. <span | |
438 | class="ptmri7t-x-x-120">Genome Biology</span>, | |
439 | 3(3):reviews1005.1–1005.6, 2002 | |
440 | <!--l. 153--><p class="noindent" >In this work <span | |
441 | class="ptmri7t-x-x-120">Vmatch </span>was used to a compute a non-redundant set from a | |
442 | large collection of protein sequences from Zea-Maize. | |
443 | </p><!--l. 155--><p class="noindent" >Similar applications are described in | |
444 | </p><!--l. 157--><p class="noindent" ><a | |
445 | id="XDON:ROY:FRE:WAL:BRE:2003"></a>Q. Dong, L. Roy, M. Freeling, V. Walbot, and V. Brendel. ZmDB, an | |
446 | integrated Database for Maize Genome Research. <span | |
447 | class="ptmri7t-x-x-120">Nucleic Acids Res.</span>, | |
448 | 31:244–247, 2003. | |
449 | ||
450 | ||
451 | ||
452 | </p></li> | |
453 | <li | |
454 | class="enumerate" id="x1-11004x2">PLEXdb is a database for gene expression resources for plants and plant | |
455 | pathogens, see | |
456 | <!--l. 166--><p class="noindent" ><a | |
457 | id="XDAS:VAN:HON:WIS:DIC:2012"></a>S. Dash, J. Van Hemert, L. Hong, R. P. Wise, and J. A. Dickerson. | |
458 | PLEXdb: gene expression resources for plants and plant pathogens. <span | |
459 | class="ptmri7t-x-x-120">Nucleic</span> | |
460 | <span | |
461 | class="ptmri7t-x-x-120">Acids Res.</span>, 40(Database issue):D1194–1201, Jan 2012 | |
462 | </p><!--l. 168--><p class="noindent" >PLEXdb provides a <span | |
463 | class="ptmri7t-x-x-120">Vmatch</span>-based <a | |
464 | href="http://www.plantgdb.org/cgi-bin/prj/PLEXdb/ProbeMatch.pl" >web-service</a> to match PLEXdb probes. | |
465 | </p></li> | |
466 | <li | |
467 | class="enumerate" id="x1-11006x3">The assembly of the Arabidopsis thaliana genome from 2004 (GenBank | |
468 | entries of 2/19/04) contained vector sequence contaminations. For example, | |
469 | region 3 617 880 to 3 625 027 of chromosome II contained a cloning vector. | |
470 | <span | |
471 | class="ptmri7t-x-x-120">Vmatch </span>was used to detect the vector contamination, see <a | |
472 | href="http://www.plantgdb.org/AtGDB/Annotation/vector.php" >here</a> | |
473 | </li> | |
474 | <li | |
475 | class="enumerate" id="x1-11008x4"><a | |
476 | id="XDON:LAW:SCHLUE:WIL:KUR:LUS:BRE:2005"></a>Q. Dong, C.J. Lawrence, S.D. Schlueter, M.D. Wilkerson, S. Kurtz, | |
477 | C. Lushbough, and V. Brendel. Comparative Plant Genomics Resources at | |
478 | PlantGDB. <span | |
479 | class="ptmri7t-x-x-120">Plant Physiology, Plant Database Focus Issue</span>, 2005 | |
480 | <!--l. 183--><p class="noindent" >This work describes PlantGDB, which provides a service called | |
481 | <a | |
482 | href="http://www.plantgdb.org/PlantGDB-cgi/vmatch/patternsearch.pl" >PatternSearch@PlantGDB</a> for genome wide pattern searches in plant | |
483 | sequences. The service is based on <span | |
484 | class="ptmri7t-x-x-120">Vmatch</span>. | |
485 | </p></li> | |
486 | <li | |
487 | class="enumerate" id="x1-11010x5"><a | |
488 | id="XLIN:KRO:2005"></a>M. Lindow and A. Krogh. Computational evidence for hundreds of | |
489 | non-conserved plant micrornas. <span | |
490 | class="ptmri7t-x-x-120">BMC Genomics</span>, 6(1):119, 2005 | |
491 | <!--l. 202--><p class="noindent" >In this work <span | |
492 | class="ptmri7t-x-x-120">Vmatch </span>was used for three different tasks: </p> | |
493 | <ul class="itemize1"> | |
494 | <li class="itemize">Searching spliced mRNA in the Arabidopsis genome to detect | |
495 | micromatches of length at least 20 with maximum 2 mismatches. | |
496 | </li> | |
497 | <li class="itemize">Finding matches of length at least 15 long with at most one mismatch | |
498 | between predicted mature miRNA-sequences and a set of ESTs as well | |
499 | as sequences from the Arabidopsis Small RNA Project (ASRP). | |
500 | </li> | |
501 | <li class="itemize">Aligning and performing single linkage clustering of the predicted | |
502 | mature miRNA sequences. Candidate pairs aligning over at least 17 | |
503 | bases, allowing an edit distance of 1 were grouped in the same family.</li></ul> | |
504 | ||
505 | ||
506 | ||
507 | </li> | |
508 | <li | |
509 | class="enumerate" id="x1-11012x6"><a | |
510 | id="XPOM:LEM:TUR:2006"></a>J.-F. Pombert, C. Lemieux, and M. Turmel. The complete chloroplast DNA | |
511 | sequence of the green alga Oltmannsiellopsis viridis reveals a distinctive | |
512 | quadripartite architecture in the chloroplast genome of early diverging ulvophytes. | |
513 | <span | |
514 | class="ptmri7t-x-x-120">BMC Biology</span>, 4:3, 2006 | |
515 | <!--l. 207--><p class="noindent" ><a | |
516 | id="XTUR:OTI:LEM:2006"></a>M. Turmel, C. Otis, and C. Lemieux. The Chloroplast Genome Sequence of | |
517 | Chara vulgaris Sheds New Light into the Closest Green Algal Relatives of Land | |
518 | Plants. <span | |
519 | class="ptmri7t-x-x-120">Molecular Biology and Evolution</span>, 23:1324–1338, 2006 | |
520 | </p><!--l. 209--><p class="noindent" >In these papers <span | |
521 | class="ptmri7t-x-x-120">Vmatch </span>was used to search and compare repeated elements in | |
522 | different chloroplast DNA. | |
523 | </p></li> | |
524 | <li | |
525 | class="enumerate" id="x1-11014x7"><a | |
526 | id="XSPA:NOU:HAA:YAN:GUN:HIN:KLE:HAB:SCHOO:MAY:2007"></a>M. Spannagl, O. Noubibou, D. Haase, L. Yang, H. Gundlach, T. Hindemitt, | |
527 | K. Klee, G. Haberer, H. Schoof, and K.F.X. Mayer. MIPSPlantsDB–plant | |
528 | database resource for integrative and comparative plant genome research. <span | |
529 | class="ptmri7t-x-x-120">Nucleic</span> | |
530 | <span | |
531 | class="ptmri7t-x-x-120">Acids Res</span>, 35(Database issue):D834–40, 2007 In this work about the | |
532 | <span | |
533 | class="ptmri7t-x-x-120">MIPSPlantsDB </span>database <span | |
534 | class="ptmri7t-x-x-120">Vmatch </span>was used to cluster large sequence | |
535 | sets. | |
536 | </li> | |
537 | <li | |
538 | class="enumerate" id="x1-11016x8"><a | |
539 | id="XSCHIJ:VOS:MAR:JON:ROS:MOL:TIK:ANG:TUN:BOV:2007"></a>E.G.W.M. Schijlen, C.H. Ric de Vos, S. Martens, H.H. Jonker, F.M. Rosin, J.W. | |
540 | Molthoff, Y.M. Tikunov, G.C. Angenent, A.J. van Tunen, and A.G. Bovy. RNA | |
541 | interference silencing of chalcone synthase, the first step in the flavonoid | |
542 | biosynthesis pathway, leads to parthenocarpic tomato fruits. <span | |
543 | class="ptmri7t-x-x-120">Plant Physiol</span>, | |
544 | 144(3):1520–30, 2007 | |
545 | <!--l. 218--><p class="noindent" >In this work <span | |
546 | class="ptmri7t-x-x-120">Vmatch </span>was used to compare target genes of the tomato Chs RNAi | |
547 | to a tomato gene index. | |
548 | </p></li> | |
549 | <li | |
550 | class="enumerate" id="x1-11018x9"><a | |
551 | id="XLIN:JAC:NYG:MAN:KRO:2007"></a>M. Lindow, A. Jacobsen, S. Nygaard, Y. Mang, and A. Krogh. Intragenomic | |
552 | matching reveals a huge potential for mirna-mediated regulation in plants. <span | |
553 | class="ptmri7t-x-x-120">PLOS</span> | |
554 | <span | |
555 | class="ptmri7t-x-x-120">Comput. Biol</span>, 3(11):e238, 2007 | |
556 | <!--l. 223--><p class="noindent" >In this work <span | |
557 | class="ptmri7t-x-x-120">Vmatch </span>was used to search different plant genomes for matches of | |
558 | length at least 20 with maximum of 2 mismatches. Here the fact that <span | |
559 | class="ptmri7t-x-x-120">Vmatch </span>is an | |
560 | exhaustive search tool is important. | |
561 | </p></li> | |
562 | <li | |
563 | class="enumerate" id="x1-11020x10"><a | |
564 | id="XDEC:OTI:THU:LEM:2007"></a>J.-C. de Cambiaire, C. Otis, M. Turmel, and C. Lemieux. The chloroplast | |
565 | ||
566 | ||
567 | ||
568 | genome sequence of the green alga leptosira terrestris: multiple losses of | |
569 | the inverted repeat and extensive genome rearrangements within the | |
570 | trebouxiophyceae. <span | |
571 | class="ptmri7t-x-x-120">BMC Genomics</span>, 8(1):213, 2007 | |
572 | <!--l. 228--><p class="noindent" >In this work <span | |
573 | class="ptmri7t-x-x-120">Vmatch </span>was used to determine the presence of shared repeated | |
574 | elements of minimum length 30, with up to 10% mismatches using in different | |
575 | sequence sets from the green alga <span | |
576 | class="ptmri7t-x-x-120">Leptosira terrestris</span>. | |
577 | </p></li> | |
578 | <li | |
579 | class="enumerate" id="x1-11022x11"><a | |
580 | id="XOSS:SCHNE:CLA:LAN:WAR:WEI:2008"></a>S. Ossowski, K. Schneeberger, R.M. Clark, C. Lanz, N. Warthmann, and | |
581 | D. Weigel. Sequencing of natural strains of Arabidopsis thaliana with short | |
582 | reads. <span | |
583 | class="ptmri7t-x-x-120">Genome Res.</span>, 18:2024–2033, 2008 | |
584 | <!--l. 235--><p class="noindent" >In this work <span | |
585 | class="ptmri7t-x-x-120">Vmatch </span>was used to map millions of short sequence reads to the | |
586 | <span | |
587 | class="ptmri7t-x-x-120">A.</span><span | |
588 | class="ptmri7t-x-x-120"> Thaliana </span>genome. Up to four mismatches and up to three indels were allowed | |
589 | in the matching process. The seed size was chosen to be 0. The reads were aligned | |
590 | using the best match strategy by iteratively increasing the the allowed number of | |
591 | mismatches and gaps at each round. | |
592 | </p></li> | |
593 | <li | |
594 | class="enumerate" id="x1-11024x12"><a | |
595 | id="XDIBO:OSS:SCHNE:RAT:2008"></a>F. De Bona, S. Ossowski, K. Schneeberger, and G. Ratsch. Optimal spliced | |
596 | alignments of short sequence reads. <span | |
597 | class="ptmri7t-x-x-120">Bioinformatics</span>, 24(16):i174–180, | |
598 | 2008 | |
599 | <!--l. 242--><p class="noindent" >In this work <span | |
600 | class="ptmri7t-x-x-120">Vmatch </span>was used to map millions of short sequence reads to the | |
601 | <span | |
602 | class="ptmri7t-x-x-120">A.</span><span | |
603 | class="ptmri7t-x-x-120"> Thaliana </span>genome. <span | |
604 | class="ptmri7t-x-x-120">Vmatch </span>was part of a multi-step pipeline, combining a fast | |
605 | matching algorithm (<span | |
606 | class="ptmri7t-x-x-120">Vmatch</span>) for initial read mapping and an optimal alignment | |
607 | algorithm based on dynamic programming (QPALMA) for high quality detection | |
608 | of splice sites. | |
609 | </p></li> | |
610 | <li | |
611 | class="enumerate" id="x1-11026x13"><a | |
612 | id="XASS:HER:LIN:HUE:TAL:SMA:IMM:ELD:FIE:SCHAT:2010"></a>A. G. L. Assunção, E. Herrero, Y-F. Lin, B. Huettel, S. Talukdar, | |
613 | C. Smaczniak, R. GH Immink, M. Van Eldik, M. Fiers, H. Schat, et al. | |
614 | Arabidopsis thaliana transcription factors bzip19 and bzip23 regulate the | |
615 | adaptation to zinc deficiency. <span | |
616 | class="ptmri7t-x-x-120">Proceedings of the National Academy of Sciences</span>, | |
617 | 107(22):10296–10301, 2010 | |
618 | <!--l. 245--><p class="noindent" >In this work <span | |
619 | class="ptmri7t-x-x-120">Vmatch </span>was used for motif searching in different plant | |
620 | genomes. | |
621 | </p></li> | |
622 | <li | |
623 | class="enumerate" id="x1-11028x14"><a | |
624 | id="XEVE:SAT:GOL:MEY:BET:SAK:WAR:JAC:2010"></a>Andrea L Eveland, Namiko Satoh-Nagasawa, Alexander Goldshmidt, Sandra | |
625 | ||
626 | ||
627 | ||
628 | Meyer, Mary Beatty, Hajime Sakai, Doreen Ware, and David Jackson. Digital | |
629 | gene expression signatures for maize development. <span | |
630 | class="ptmri7t-x-x-120">Plant physiology</span>, | |
631 | 154(3):1024–1039, 2010 | |
632 | <!--l. 248--><p class="noindent" >In this work <span | |
633 | class="ptmri7t-x-x-120">Vmatch </span>was used to map unique consensus sequence tags to the | |
634 | maize reference genome. | |
635 | </p></li> | |
636 | <li | |
637 | class="enumerate" id="x1-11030x15"><a | |
638 | id="XBRO:OTI:LEM:TUR:2010"></a>Jean-Simon Brouard, Christian Otis, Claude Lemieux, and Monique Turmel. The | |
639 | exceptionally large chloroplast genome of the green alga floydiella terrestris | |
640 | illuminates the evolutionary history of the chlorophyceae. <span | |
641 | class="ptmri7t-x-x-120">Genome biology and</span> | |
642 | <span | |
643 | class="ptmri7t-x-x-120">evolution</span>, 2:240, 2010 | |
644 | <!--l. 252--><p class="noindent" >In this work <span | |
645 | class="ptmri7t-x-x-120">Vmatch </span>was used to identify and cluster repeated sequences in | |
646 | <span | |
647 | class="ptmri7t-x-x-120">Floydiella </span>chloroplast genome. | |
648 | </p></li> | |
649 | <li | |
650 | class="enumerate" id="x1-11032x16"><a | |
651 | id="XREH:AQU:GRU:HEN:HIL:LAU:NAO:PAT:ROM:SHU:2010"></a>Hubert Rehrauer, Catharine Aquino, Wilhelm Gruissem, Stefan R Henz, Pierre | |
652 | Hilson, Sascha Laubinger, Naira Naouar, Andrea Patrignani, Stephane Rombauts, | |
653 | Huan Shu, et al. Agronomics1: a new resource for arabidopsis transcriptome | |
654 | profiling. <span | |
655 | class="ptmri7t-x-x-120">Plant Physiology</span>, 152(2):487–499, 2010 | |
656 | <!--l. 257--><p class="noindent" >In this work <span | |
657 | class="ptmri7t-x-x-120">Vmatch </span>was used to calculate direct and reverse complementary | |
658 | matches of length 17 bp or greater with edit distance 1 or less between | |
659 | five nuclear chromosomes and mitochondrial and chloroplast genome | |
660 | sequences. | |
661 | </p></li> | |
662 | <li | |
663 | class="enumerate" id="x1-11034x17"><a | |
664 | id="XSEK:LIN:CHI:HAN:BUE:LEO:KAE:2011"></a>R. S. Sekhon, H. Lin, K. L. Childs, C. N. Hansey, C. R. Buell, N. de Leon, | |
665 | and S. M. Kaeppler. Genome-wide atlas of transcription during maize | |
666 | development. <span | |
667 | class="ptmri7t-x-x-120">Plant J.</span>, 66(4):553–563, May 2011 | |
668 | <!--l. 261--><p class="noindent" >In this work <span | |
669 | class="ptmri7t-x-x-120">Vmatch </span>was used to search probe sequences against the maize | |
670 | genome the cDNA sequences of the official maize gene models. | |
671 | </p></li> | |
672 | <li | |
673 | class="enumerate" id="x1-11036x18"><a | |
674 | id="XDAS:OH:HAA:HER:HON:ALI:YUN:BRE:ZHU:BOH:2011"></a>M. Dassanayake, D. H. Oh, J. S. Haas, A. Hernandez, H. Hong, S. Ali, D. J. | |
675 | Yun, R. A. Bressan, J. K. Zhu, H. J. Bohnert, and J. M. Cheeseman. The | |
676 | genome of the extremophile crucifer Thellungiella parvula. <span | |
677 | class="ptmri7t-x-x-120">Nat. Genet.</span>, | |
678 | 43(9):913–918, Sep 2011 | |
679 | <!--l. 266--><p class="noindent" >In this work <span | |
680 | class="ptmri7t-x-x-120">Vmatch </span>was used for clustering sequences assembled from 454-reads | |
681 | ||
682 | ||
683 | ||
684 | of <span | |
685 | class="ptmri7t-x-x-120">Thellungiella parvula</span>, a model for the evolution of plant adaptation to extreme | |
686 | environments. | |
687 | </p></li> | |
688 | <li | |
689 | class="enumerate" id="x1-11038x19"><a | |
690 | id="XWIL:HOF:KLE:WEI:2011"></a>E. M. Willing, M. Hoffmann, J. D. Klein, D. Weigel, and C. Dreyer. | |
691 | Paired-end RAD-seq for de novo assembly and marker design without available | |
692 | reference. <span | |
693 | class="ptmri7t-x-x-120">Bioinformatics</span>, 27(16):2187–2193, Aug 2011 | |
694 | <!--l. 270--><p class="noindent" >In this work <span | |
695 | class="ptmri7t-x-x-120">Vmatch </span>was used for grouping short reads into pools representing | |
696 | the same RAD tag. | |
697 | </p></li> | |
698 | <li | |
699 | class="enumerate" id="x1-11040x20"><a | |
700 | id="XGAO:ZHO:WAN:SU:WAN:2011"></a>L. Gao, Y. Zhou, Z.-W. Wang, Y.-J. Su, and T. Wang. Evolution of the | |
701 | <span | |
702 | class="ptmri7t-x-x-120">rpoB-psbZ </span>region in fern plastid genomes: notable structural rearrangements | |
703 | and highly variable intergenic spacers. <span | |
704 | class="ptmri7t-x-x-120">BMC Plant Biology</span>, 11(1):64, | |
705 | 2011 | |
706 | <!--l. 274--><p class="noindent" >In this work <span | |
707 | class="ptmri7t-x-x-120">Vmatch </span>was used for detecting and clustering repetitive sequences in | |
708 | diverse fern plastid genomes. | |
709 | </p></li> | |
710 | <li | |
711 | class="enumerate" id="x1-11042x21"><a | |
712 | id="XSLO:ALV:CHU:WU:MCC:PAL:TAY:2012"></a>D. B. Sloan, A. J. Alverson, J. P. Chuckalovcak, M. Wu, D. E. McCauley, | |
713 | J. D. Palmer, and D. R. Taylor. Rapid evolution of enormous, multichromosomal | |
714 | genomes in flowering plant mitochondria with exceptionally high mutation rates. | |
715 | <span | |
716 | class="ptmri7t-x-x-120">PLoS Biol.</span>, 10(1):e1001241, Jan 2012 | |
717 | <!--l. 278--><p class="noindent" >In this work <span | |
718 | class="ptmri7t-x-x-120">Vmatch </span>was used to precisely define the boundaries of all repeats | |
719 | with 100% sequence identity. | |
720 | </p></li> | |
721 | <li | |
722 | class="enumerate" id="x1-11044x22"><a | |
723 | id="XDUB:FAR:SCHLU:CAN:ABE:TUT:WOO:SHA:MUL:KUD:2011"></a>Anuja Dubey, Andrew Farmer, Jessica Schlueter, Steven B Cannon, Brian | |
724 | Abernathy, Reetu Tuteja, Jimmy Woodward, Trushar Shah, Benjamin | |
725 | Mulasmanovic, Himabindu Kudapa, et al. Defining the transcriptome | |
726 | assembly and its use for genome dynamics and transcriptome profiling | |
727 | studies in pigeonpea (<span | |
728 | class="ptmri7t-x-x-120">Cajanus cajan </span>l.). <span | |
729 | class="ptmri7t-x-x-120">DNA research</span>, 18(3):153–164, | |
730 | 2011 | |
731 | <!--l. 281--><p class="noindent" >In this work <span | |
732 | class="ptmri7t-x-x-120">Vmatch </span>was used cluster sequences based on their six-frame | |
733 | translation. | |
734 | </p></li> | |
735 | <li | |
736 | class="enumerate" id="x1-11046x23"><a | |
737 | id="XSAX:PEN:UPA:KUM:CAR:SCHLU:FAR:WHA:SAR:MAY:2012"></a>Rachit K Saxena, R Varma Penmetsa, Hari D Upadhyaya, Ashish Kumar, | |
738 | ||
739 | ||
740 | ||
741 | Noelia Carrasquilla-Garcia, Jessica A Schlueter, Andrew Farmer, Adam M | |
742 | Whaley, Birinchi K Sarma, Gregory D May, et al. Large-scale development of | |
743 | cost-effective single-nucleotide polymorphism marker assays for genetic | |
744 | mapping in pigeonpea and comparative mapping in legumes. <span | |
745 | class="ptmri7t-x-x-120">DNA research</span>, | |
746 | 19(6):449–461, 2012 | |
747 | <!--l. 285--><p class="noindent" >In this work <span | |
748 | class="ptmri7t-x-x-120">Vmatch </span>was used to identify reciprocal best matches between the | |
749 | pigeonpea sequences and other legume sequences. | |
750 | </p></li> | |
751 | <li | |
752 | class="enumerate" id="x1-11048x24"><a | |
753 | id="XHAZ:REE:RIS:PEC:2012"></a>B. Z. Haznedaroglu, D. Reeves, H. Rismani-Yazdi, and J. Peccia. Optimization | |
754 | of de novo transcriptome assembly from high-throughput short read sequencing | |
755 | data improves functional annotation for non-model organisms. <span | |
756 | class="ptmri7t-x-x-120">BMC</span> | |
757 | <span | |
758 | class="ptmri7t-x-x-120">Bioinformatics</span>, 13:170, 2012 | |
759 | <!--l. 290--><p class="noindent" >In this work <span | |
760 | class="ptmri7t-x-x-120">Vmatch </span>was used for assembly clustering and optimization | |
761 | of contigs for <span | |
762 | class="ptmri7t-x-x-120">Neochloris oleoabundans </span>(a Chlorophyceae class green | |
763 | microalgae). | |
764 | </p></li> | |
765 | <li | |
766 | class="enumerate" id="x1-11050x25"><a | |
767 | id="XMAR:KLE:BAN:BLA:MAC:SCHMU:SCHOL:GUN:WIC:SIM:2012"></a>M. M. Martis, S. Klemme, A. M. Banaei-Moghaddam, F. R. Blattner, | |
768 | J. Macas, T. Schmutzer, U. Scholz, H. Gundlach, T. Wicker, H. Šimková, | |
769 | P. Novak, P. Neumann, M. Kubalakova, E. Bauer, G. Haseneyer, J. Fuchs, | |
770 | J. Dolezel, N. Stein, K. F. Mayer, and A. Houben. Selfish supernumerary | |
771 | chromosome reveals its origin as a mosaic of host genome and organellar | |
772 | sequences. <span | |
773 | class="ptmri7t-x-x-120">Proc. Natl. Acad. Sci. U.S.A.</span>, 109(33):13343–13346, Aug | |
774 | 2012 | |
775 | <!--l. 294--><p class="noindent" >In this work <span | |
776 | class="ptmri7t-x-x-120">Vmatch </span>was used to match reads against a repeat library to identity | |
777 | the content of the repetitive DNA per sequence read. | |
778 | </p></li> | |
779 | <li | |
780 | class="enumerate" id="x1-11052x26"><a | |
781 | id="XCHI:DAV:BUE:2011"></a>K. L. Childs, R. M. Davidson, and C. R. Buell. Gene coexpression network | |
782 | analysis as a source of functional annotation for rice genes. <span | |
783 | class="ptmri7t-x-x-120">PloS one</span>, | |
784 | 6(7):e22196, 2011 | |
785 | <!--l. 297--><p class="noindent" >In this work <span | |
786 | class="ptmri7t-x-x-120">Vmatch </span>was used to align individual probes to representative gene | |
787 | models. | |
788 | </p></li> | |
789 | <li | |
790 | class="enumerate" id="x1-11054x27"><a | |
791 | id="XSEV:DIJ:HAM:2011"></a>E. I. Severing, A. D. J. van Dijk, and R. C. H. J. van Ham. Assessing the | |
792 | contribution of alternative splicing to proteome diversity in arabidopsis thaliana | |
793 | ||
794 | ||
795 | ||
796 | using proteomics data. <span | |
797 | class="ptmri7t-x-x-120">BMC Plant Biology</span>, 11(1):82, 2011 | |
798 | <!--l. 301--><p class="noindent" >In this work <span | |
799 | class="ptmri7t-x-x-120">Vmatch </span>was used for performing exact searches with peptides | |
800 | against the filtered proteome of <span | |
801 | class="ptmri7t-x-x-120">A. thaliana</span>. | |
802 | </p></li> | |
803 | <li | |
804 | class="enumerate" id="x1-11056x28"><a | |
805 | id="XWOL:WEI:SEG:ROS:BEI:DON:SPI:NOR:REH:KOE:2011"></a>P. Wolff, I. Weinhofer, J. Seguin, P. Roszak, C. Beisel, M.T. Donoghue, | |
806 | C. Spillane, M. Nordborg, M. Rehmsmeier, and C. Köhler. High-resolution | |
807 | analysis of parent-of-origin allelic expression in the arabidopsis endosperm. <span | |
808 | class="ptmri7t-x-x-120">PLoS</span> | |
809 | <span | |
810 | class="ptmri7t-x-x-120">Genet</span>, 7(6):e1002126–e1002126, 2011 | |
811 | <!--l. 307--><p class="noindent" >In this work <span | |
812 | class="ptmri7t-x-x-120">Vmatch </span>was used to map RNAseq reads, allowing up to two | |
813 | mismatches (option <span | |
814 | class="cmtt-12">-h 2</span>) and generating maximal substring matches that are | |
815 | unique in some reference dataset (option <span | |
816 | class="cmtt-12">-mum cand</span>). | |
817 | </p></li> | |
818 | <li | |
819 | class="enumerate" id="x1-11058x29"><a | |
820 | id="XFLE:KHA:JOH:YOU:MIT:WRE:HES:FOS:SCHAR:SCO:2011"></a>D. J. Fleetwood, A. K. Khan, R. D. Johnson, C. A. Young, S. Mittal, R. E. | |
821 | Wrenn, U. Hesse, S. J. Foster, C. L. Schardl, and B. Scott. Abundant | |
822 | degenerate miniature inverted-repeat transposable elements in genomes of | |
823 | epichloid fungal endophytes of grasses. <span | |
824 | class="ptmri7t-x-x-120">Genome Biol Evol</span>, 3:1253–1264, | |
825 | 2011 | |
826 | <!--l. 312--><p class="noindent" >In this work <span | |
827 | class="ptmri7t-x-x-120">Vmatch </span>was used to identify terminal inverted repeats of length | |
828 | range 10-65 bp, <span | |
829 | class="zptmcm7y-x-x-120">≥ </span><span | |
830 | class="zptmcm7t-x-x-120">80% </span>identity, maximum inter-TIR distance 650 bp in in | |
831 | genomes of epichloid fungal endophytes of grasses. | |
832 | </p></li> | |
833 | <li | |
834 | class="enumerate" id="x1-11060x30"><a | |
835 | id="XCHI:KON:BUE:2012"></a>K. L. Childs, K. Konganti, and C. R. Buell. The Biofuel Feedstock Genomics | |
836 | Resource: a web-based portal and database to enable functional genomics | |
837 | of plant biofuel feedstock species. <span | |
838 | class="ptmri7t-x-x-120">Database (Oxford)</span>, 2012:bar061, | |
839 | 2012 | |
840 | <!--l. 315--><p class="noindent" >In this work <span | |
841 | class="ptmri7t-x-x-120">Vmatch </span>was used to match putative unique transcript sequence | |
842 | assemblies. | |
843 | </p></li> | |
844 | <li | |
845 | class="enumerate" id="x1-11062x31"><a | |
846 | id="XCHE:CAS:BAI:RED:MIC:2012"></a>Y. Chen, B. J. Cassone, X. Bai, M. G. Redinbaugh, and A. P. Michel. | |
847 | Transcriptome of the plant virus vector Graminella nigrifrons, and the molecular | |
848 | interactions of maize fine streak rhabdovirus transmission. <span | |
849 | class="ptmri7t-x-x-120">PLoS ONE</span>, | |
850 | 7(7):e40613, 2012 | |
851 | <!--l. 319--><p class="noindent" >In this work <span | |
852 | class="ptmri7t-x-x-120">Vmatch </span>was used for refining assemblies of Illumina reads in | |
853 | ||
854 | ||
855 | ||
856 | the context of a transcriptome project for plant virus vector <span | |
857 | class="ptmri7t-x-x-120">Graminella</span> | |
858 | <span | |
859 | class="ptmri7t-x-x-120">nigrifrons</span>. | |
860 | </p></li> | |
861 | <li | |
862 | class="enumerate" id="x1-11064x32"><a | |
863 | id="XKRI:PAT:JAI:GAU:CHOU:VAI:DEE:HAR:KRI:NAI:2012"></a>N. M. Krishnan, S. Pattnaik, P. Jain, P. Gaur, R. Choudhary, S. Vaidyanathan, | |
864 | S. Deepak, A. K. Hariharan, P. B. Krishna, J. Nair, L. Varghese, N. K. | |
865 | Valivarthi, K. Dhas, K. Ramaswamy, and B. Panda. A draft of the genome and | |
866 | four transcriptomes of a medicinal and pesticidal angiosperm Azadirachta indica. | |
867 | <span | |
868 | class="ptmri7t-x-x-120">BMC Genomics</span>, 13:464, 2012 | |
869 | <!--l. 324--><p class="noindent" >In this work <span | |
870 | class="ptmri7t-x-x-120">Vmatch </span>was used for clustering repeats and for building a consensus | |
871 | repeat library in the context of genome and transcriptome projects for <span | |
872 | class="ptmri7t-x-x-120">Azadirachta</span> | |
873 | <span | |
874 | class="ptmri7t-x-x-120">indica</span>, a medicinal and pesticidal angiosperm. | |
875 | </p></li> | |
876 | <li | |
877 | class="enumerate" id="x1-11066x33"><a | |
878 | id="XLIU:KUM:ZHA:ZHE:WAR:2012"></a>Z. Liu, S. Kumari, L. Zhang, Y. Zheng, and D. Ware. Characterization of | |
879 | mirnas in response to short-term waterlogging in three inbred lines of zea mays. | |
880 | <span | |
881 | class="ptmri7t-x-x-120">PLoS One</span>, 7(6):e39786, 2012 | |
882 | <!--l. 328--><p class="noindent" >In this work <span | |
883 | class="ptmri7t-x-x-120">Vmatch </span>was used to map unique consensus sequences tags to the | |
884 | maize reference genome and to predict targets of novel miRNAs. | |
885 | </p></li> | |
886 | <li | |
887 | class="enumerate" id="x1-11068x34"><a | |
888 | id="XBOU:KOU:PAV:MIN:TSA:DAR:2012"></a>A. Bousios, Y. A. I. Kourmpetis, P. Pavlidis, E. Minga, A. Tsaftaris, and | |
889 | N. Darzentas. The turbulent life of sirevirus retrotransposons and the evolution of | |
890 | the maize genome: more than ten thousand elements tell the story. <span | |
891 | class="ptmri7t-x-x-120">The Plant</span> | |
892 | <span | |
893 | class="ptmri7t-x-x-120">Journal</span>, 69(3):475–488, 2012 | |
894 | <!--l. 331--><p class="noindent" >In this work <span | |
895 | class="ptmri7t-x-x-120">Vmatch </span>was used for masking Long Terminal Repeats in the Maize | |
896 | Genome Sequence. | |
897 | </p></li> | |
898 | <li | |
899 | class="enumerate" id="x1-11070x35">In the papers | |
900 | <!--l. 335--><p class="noindent" ><a | |
901 | id="XHER:MAR:DOR:PFE:GAL:SCHAA:JOU:SIM:VAL:DOL:2012"></a>P. Hernandez, M. Martis, G. Dorado, M. Pfeifer, S. Galvez, S. Schaaf, N. Jouve, | |
902 | H. Šimková, M. Valarik, J. Dolezel, and K. F. Mayer. Next-generation | |
903 | sequencing and syntenic integration of flow-sorted arms of wheat chromosome | |
904 | 4A exposes the chromosome structure and gene content. <span | |
905 | class="ptmri7t-x-x-120">Plant J.</span>, 69(3):377–386, | |
906 | Feb 2012 | |
907 | </p><!--l. 337--><p class="noindent" ><a | |
908 | id="XPHI:PAU:BER:SOU:CHO:LAU:SIM:SAF:BEL:VAU:2013"></a>R. Philippe, E. Paux, I. Bertin, P. Sourdille, F. Choulet, C. Laugier, | |
909 | H. Šimková, J. Šafář, A. Bellec, S. Vautrin, et al. A high density physical map | |
910 | ||
911 | ||
912 | ||
913 | of chromosome 1bl supports evolutionary studies, map-based cloning and | |
914 | sequencing in wheat. <span | |
915 | class="ptmri7t-x-x-120">Genome Biol</span>, 14(6):R64, 2013 | |
916 | </p><!--l. 339--><p class="noindent" ><span | |
917 | class="ptmri7t-x-x-120">Vmatch </span>was used to mask repetitive DNA. | |
918 | </p></li> | |
919 | <li | |
920 | class="enumerate" id="x1-11072x36"><a | |
921 | id="XHOW:YU:KNA:CRO:KOL:DOL:LOR:DEA:2013"></a>G. T. Howe, J. Yu, B. Knaus, R. Cronn, S. Kolpak, P. Dolan, W. W. Lorenz, | |
922 | and J. F. Dean. A SNP resource for Douglas-fir: de novo transcriptome | |
923 | assembly and SNP detection and validation. <span | |
924 | class="ptmri7t-x-x-120">BMC Genomics</span>, 14:137, | |
925 | 2013 | |
926 | <!--l. 342--><p class="noindent" >In this work <span | |
927 | class="ptmri7t-x-x-120">Vmatch </span>was used to cluster 40 010 assembled isotigs. | |
928 | </p></li> | |
929 | <li | |
930 | class="enumerate" id="x1-11074x37"><a | |
931 | id="XKAR:HAA:MAL:GEE:BOV:LAM:ANG:MAA:2013"></a>R. Karlova, J. C. van Haarst, C. Maliepaard, H. van de Geest, A. G. Bovy, | |
932 | M. Lammers, G. C. Angenent, and R. A. de Maagd. Identification of | |
933 | microRNA targets in tomato fruit development using high-throughput | |
934 | sequencing and degradome analysis. <span | |
935 | class="ptmri7t-x-x-120">J. Exp. Bot.</span>, 64(7):1863–1878, Apr | |
936 | 2013 | |
937 | <!--l. 346--><p class="noindent" >In this work <span | |
938 | class="ptmri7t-x-x-120">Vmatch </span>was used to preprocess short reads in the context of | |
939 | identifying mircoRNA targets in tomato fruit development. | |
940 | </p></li> | |
941 | <li | |
942 | class="enumerate" id="x1-11076x38"><a | |
943 | id="XGRO:MAR:SIM:ABR:WAN:VIS:2013"></a>S. M. Gross, J. A. Martin, J. Simpson, M. J. Abraham-Juarez, Z. Wang, and | |
944 | A. Visel. De novo transcriptome assembly of drought tolerant CAM | |
945 | plants, Agave deserti and Agave tequilana. <span | |
946 | class="ptmri7t-x-x-120">BMC Genomics</span>, 14:563, | |
947 | 2013 | |
948 | <!--l. 351--><p class="noindent" >In this work <span | |
949 | class="ptmri7t-x-x-120">Vmatch </span>was used in an all-vs-all comparison to bin contigs into loci | |
950 | based on a minimum of 200 bp sequence overlap in the context of transcriptome | |
951 | assembly for two Agave-species. | |
952 | </p></li> | |
953 | <li | |
954 | class="enumerate" id="x1-11078x39"><a | |
955 | id="XKAN:HEL:DUR:WIN:ENG:BEH:HOL:BRA:HAU:FER:2013"></a>U. Kanter, W. Heller, J. Durner, J. B. Winkler, M. Engel, H. Behrendt, | |
956 | A. Holzinger, P. Braun, M. Hauser, F. Ferreira, K. Mayer, M. Pfeifer, and | |
957 | D. Ernst. Molecular and immunological characterization of ragweed (Ambrosia | |
958 | artemisiifolia L.) pollen after exposure of the plants to elevated ozone over a | |
959 | whole growing season. <span | |
960 | class="ptmri7t-x-x-120">PLoS ONE</span>, 8(4):e61518, 2013 | |
961 | <!--l. 354--><p class="noindent" >In this work <span | |
962 | class="ptmri7t-x-x-120">Vmatch </span>was used to align 454-reads to assembled isotigs for | |
963 | Ragweed pollen. | |
964 | ||
965 | ||
966 | ||
967 | </p></li> | |
968 | <li | |
969 | class="enumerate" id="x1-11080x40"><a | |
970 | id="XKUG:SIE:NUS:AME:SPAN:STEI:LEM:MAY:BUE:SCHWE:2013"></a>K. G. Kugler, G. Siegwart, T. Nussbaumer, C. Ametz, M. Spannagl, | |
971 | B. Steiner, M. Lemmens, K. F. X. Mayer, H. Buerstmayr, and W. Schweiger. | |
972 | Quantitative trait loci-dependent analysis of a gene co-expression network | |
973 | associated with fusarium head blight resistance in bread wheat (triticum aestivum | |
974 | l.). <span | |
975 | class="ptmri7t-x-x-120">BMC Genomics</span>, 14(1):728, 2013 | |
976 | <!--l. 357--><p class="noindent" >In this work <span | |
977 | class="ptmri7t-x-x-120">Vmatch </span>was used for comparing gene sets. | |
978 | </p></li> | |
979 | <li | |
980 | class="enumerate" id="x1-11082x41"><a | |
981 | id="XMAR:ZHO:HAS:SCHMU:VRA:KUB:KOEN:KUG:SCHOL:HAC:2013"></a>Mihaela M Martis, Ruonan Zhou, Grit Haseneyer, Thomas Schmutzer, Jan | |
982 | Vrána, Marie Kubaláková, Susanne König, Karl G Kugler, Uwe Scholz, Bernd | |
983 | Hackauf, et al. Reticulate evolution of the rye genome. <span | |
984 | class="ptmri7t-x-x-120">The Plant Cell</span>, | |
985 | 25(10):3685–3698, 2013 | |
986 | <!--l. 361--><p class="noindent" >In this work <span | |
987 | class="ptmri7t-x-x-120">Vmatch </span>was used to detect repetitive DNA content of chromosomal | |
988 | survey sequences from the Rye genome. | |
989 | </p></li> | |
990 | <li | |
991 | class="enumerate" id="x1-11084x42">In the papers | |
992 | <!--l. 366--><p class="noindent" ><a | |
993 | id="XKOP:MAR:VHA:HRV:VRA:BAR:KOP:CAT:STO:NOV:2013"></a>D. Kopeckỳ, M. Martis, J. Číhalíková, E. Hřibová, J. Vrána, J. Bartoš, | |
994 | J. Kopecká, F. Cattonaro, Š. Stočes, Petr Novák, et al. Flow sorting and | |
995 | sequencing meadow fescue chromosome 4f. <span | |
996 | class="ptmri7t-x-x-120">Plant Physiology</span>, 163(3):1323–1337, | |
997 | 2013 | |
998 | </p><!--l. 368--><p class="noindent" ><a | |
999 | id="XKOP:MAR:CHA:HRI:VRA:BAR:2013"></a>D. Kopeckỳ, M Martis, J Číhalíková, E Hřibová, J Vrána, J Bartoš, et al. | |
1000 | Genomics of meadow fescue chromosome 4f. <span | |
1001 | class="ptmri7t-x-x-120">Plant Physiol</span>, 163:1323–1337, | |
1002 | 2013 | |
1003 | </p><!--l. 370--><p class="noindent" ><span | |
1004 | class="ptmri7t-x-x-120">Vmatch </span>was used for identifying repetitive DNA content in contigs of meadow | |
1005 | fescue chromosome 4F assembled from Illumina short reads. | |
1006 | </p></li> | |
1007 | <li | |
1008 | class="enumerate" id="x1-11086x43">In the papers | |
1009 | <!--l. 377--><p class="noindent" ><a | |
1010 | id="XJAY:WAN:YU:TAC:PEL:COL:REN:VOI:2011"></a>F. Jay, Y. Wang, A. Yu, L. Taconnat, S. Pelletier, V. Colot, J.-P. Renou, and | |
1011 | O. Voinnet. Misregulation of <span | |
1012 | class="ptmri7t-x-x-120">AUXIN RESPONSE FACTOR 8 </span>underlies the | |
1013 | developmental abnormalities caused by three distinct viral silencing | |
1014 | suppressors in <span | |
1015 | class="ptmri7t-x-x-120">Arabidopsis</span>. <span | |
1016 | class="ptmri7t-x-x-120">PLoS Pathog</span>, 7(5):e1002035–e1002035, | |
1017 | 2011 | |
1018 | </p><!--l. 379--><p class="noindent" ><a | |
1019 | id="XWAN:WEI:SMI:2013"></a>X. Wang, D. Weigel, and L. M. Smith. Transposon variants and their | |
1020 | ||
1021 | ||
1022 | ||
1023 | effects on gene expression in arabidopsis. <span | |
1024 | class="ptmri7t-x-x-120">PLoS Genet</span>, 9(2):e1003255, | |
1025 | 2013 | |
1026 | </p><!--l. 381--><p class="noindent" ><span | |
1027 | class="ptmri7t-x-x-120">Vmatch </span>was used for mapping siRNA sequences to the <span | |
1028 | class="ptmri7t-x-x-120">Arabidopsis thaliana</span> | |
1029 | genome. | |
1030 | </p></li> | |
1031 | <li | |
1032 | class="enumerate" id="x1-11088x44"><a | |
1033 | id="XHEN:VIV:DES:CHAU:PAY:GUT:CAS:2014"></a>E. Henaff, C. Vives, B. Desvoyes, A. Chaurasia, J. Payet, C. Gutierrez, and | |
1034 | J. M. Casacuberta. Extensive amplification of the E2F transcription factor | |
1035 | binding sites by transposons during evolution of Brassica species. <span | |
1036 | class="ptmri7t-x-x-120">Plant J.</span>, | |
1037 | 77(6):852–862, Mar 2014 | |
1038 | <!--l. 385--><p class="noindent" >In this work <span | |
1039 | class="ptmri7t-x-x-120">Vmatch </span>was used for the identification of binding motifs. | |
1040 | </p></li> | |
1041 | <li | |
1042 | class="enumerate" id="x1-11090x45"><a | |
1043 | id="XWAN:HAB:GUN:GLAE:NUS:LUO:LOM:BOR:KER:SHA:2014"></a>W Wang, G Haberer, H Gundlach, C Gläßer, TCLM Nussbaumer, | |
1044 | MC Luo, A Lomsadze, M Borodovsky, RA Kerstetter, J Shanklin, | |
1045 | et al. The <span | |
1046 | class="ptmri7t-x-x-120">Spirodela polyrhiza </span>genome reveals insights into its neotenous | |
1047 | reduction fast growth and aquatic lifestyle. <span | |
1048 | class="ptmri7t-x-x-120">Nature Communications</span>, 5, | |
1049 | 2014 | |
1050 | <!--l. 390--><p class="noindent" >In this work <span | |
1051 | class="ptmri7t-x-x-120">Vmatch </span>was used for masking one sequence set with another and for | |
1052 | mapping miRNA sequences of all plant species present in a reference database to | |
1053 | whole-genome assembly of <span | |
1054 | class="ptmri7t-x-x-120">Spirodela polyrhiza</span>. | |
1055 | </p></li> | |
1056 | <li | |
1057 | class="enumerate" id="x1-11092x46"><a | |
1058 | id="XLOG:SCHEL:NUR:SAM:PEN:2014"></a>M. D. Logacheva, M. I. Schelkunov, M. S. Nuraliev, T. H. Samigullin, and | |
1059 | A. A. Penin. The plastid genome of mycoheterotrophic monocot petrosavia | |
1060 | stellaris exhibits both gene losses and multiple rearrangements. <span | |
1061 | class="ptmri7t-x-x-120">Genome biology</span> | |
1062 | <span | |
1063 | class="ptmri7t-x-x-120">and evolution</span>, 6(1):238–246, 2014 | |
1064 | <!--l. 393--><p class="noindent" >In this work <span | |
1065 | class="ptmri7t-x-x-120">Vmatch </span>was used for repeat detection. | |
1066 | </p></li> | |
1067 | <li | |
1068 | class="enumerate" id="x1-11094x47"><a | |
1069 | id="XWAN:SHI:RIN:2015"></a>X. Wang, W. Shi, and T. Rinehart. Transcriptomes That Confer to Plant Defense | |
1070 | against Powdery Mildew Disease in Lagerstroemia indica. <span | |
1071 | class="ptmri7t-x-x-120">Int J Genomics</span>, | |
1072 | 2015:528395, 2015 | |
1073 | <!--l. 397--><p class="noindent" >In this work <span | |
1074 | class="ptmri7t-x-x-120">Vmatch </span>was used to eliminate redundancies in assemblies of | |
1075 | Illumina reads in the context of studying plant defense mechanisms. | |
1076 | </p></li> | |
1077 | <li | |
1078 | class="enumerate" id="x1-11096x48"><a | |
1079 | id="XASH:HUL:WAN:YAN:GUA:JON:MAT:MOC:CHE:STE:2015"></a>H. Ashrafi, A. M. Hulse-Kemp, F. Wang, S. S. Yang, X. Guan, D. C. Jones, | |
1080 | ||
1081 | ||
1082 | ||
1083 | M. Matvienko, K. Mockaitis, Z. J. Chen, D. M. Stelly, et al. A long-read | |
1084 | transcriptome assembly of cotton (l.) and intraspecific single nucleotide | |
1085 | polymorphism discovery. <span | |
1086 | class="ptmri7t-x-x-120">The Plant Genome</span>, 2015 | |
1087 | <!--l. 400--><p class="noindent" >In this work <span | |
1088 | class="ptmri7t-x-x-120">Vmatch </span>was used for clustering to determine a non-redundant set of | |
1089 | assembled contigs. | |
1090 | </p></li> | |
1091 | <li | |
1092 | class="enumerate" id="x1-11098x49"><a | |
1093 | id="XUST:NOV:BLI:SMY:2015"></a>K. Ustyantsev, O. Novikova, A. Blinov, and G. Smyshlyaev. Convergent | |
1094 | evolution of ribonuclease h in ltr retrotransposons and retroviruses. <span | |
1095 | class="ptmri7t-x-x-120">Molecular</span> | |
1096 | <span | |
1097 | class="ptmri7t-x-x-120">biology and evolution</span>, 32(5):1197–1207, 2015 | |
1098 | <!--l. 403--><p class="noindent" >In this work <span | |
1099 | class="ptmri7t-x-x-120">Vmatch </span>was used for clustering sequences based on their RT and | |
1100 | aRNH domain. | |
1101 | </p></li> | |
1102 | <li | |
1103 | class="enumerate" id="x1-11100x50"><a | |
1104 | id="XHLE:RIV:CLA:MAR:VAN:GON:GAR:LER:SIM:VAL:2015"></a>M. Helguera, M. Rivarola, B. Clavijo, M. M. Martis, L. S. Vanzetti, | |
1105 | S. González, I. Garbus, P. Leroy, H. Šimková, M. Valárik, et al. New insights | |
1106 | into the wheat chromosome 4d structure and virtual gene order, revealed by | |
1107 | survey pyrosequencing. <span | |
1108 | class="ptmri7t-x-x-120">Plant Science</span>, 233:200–212, 2015 | |
1109 | <!--l. 406--><p class="noindent" >In this work <span | |
1110 | class="ptmri7t-x-x-120">Vmatch </span>was used for identifying repeats in contigs assembled from | |
1111 | 454-reads. | |
1112 | </p></li> | |
1113 | <li | |
1114 | class="enumerate" id="x1-11102x51"><a | |
1115 | id="XSHE:YAN:LU:WAN:SON:2015"></a>Qi Shen, Jun Yang, Chaolong Lu, Bo Wang, and Chi Song. The complete | |
1116 | chloroplast genome sequence of perilla frutescens (l.). <span | |
1117 | class="ptmri7t-x-x-120">Mitochondrial DNA</span>, | |
1118 | preprint:1–2, 2015 | |
1119 | <!--l. 409--><p class="noindent" >In this work <span | |
1120 | class="ptmri7t-x-x-120">Vmatch </span>was used for identifying inverted repeats in chloroplast | |
1121 | genomes. | |
1122 | </p></li> | |
1123 | <li | |
1124 | class="enumerate" id="x1-11104x52"><a | |
1125 | id="XPAN:MOH:KHA:MEH:EBR:2015"></a>Bahman Panahi, Seyed Abolghasem Mohammadi, Reyhaneh Ebrahimi | |
1126 | Khaksefidi, Jalil Fallah Mehrabadi, and Esmaeil Ebrahimie. Genome-wide | |
1127 | analysis of alternative splicing events in <span | |
1128 | class="ptmri7t-x-x-120">Hordeum vulgare</span>: Highlighting retention | |
1129 | of intron-based splicing and its possible function through network analysis. <span | |
1130 | class="ptmri7t-x-x-120">FEBS</span> | |
1131 | <span | |
1132 | class="ptmri7t-x-x-120">letters</span>, 589(23):3564–3575, 2015 | |
1133 | <!--l. 413--><p class="noindent" >In this work <span | |
1134 | class="ptmri7t-x-x-120">Vmatch </span>was used to identify contaminations and repetitive | |
1135 | elements by comparison of mRNA sequences to vector, bacterial and repeat | |
1136 | databases. | |
1137 | ||
1138 | ||
1139 | ||
1140 | </p></li> | |
1141 | <li | |
1142 | class="enumerate" id="x1-11106x53"><a | |
1143 | id="XWOL:TWO:GAD:KNA:GRU:GEN:2015"></a>SN Wolfenbarger, MC Twomey, DM Gadoury, BJ Knaus, NJ Grünwald, and | |
1144 | DH Gent. Identification and distribution of mating-type idiomorphs in | |
1145 | populations of podosphaera macularis and development of chasmothecia of the | |
1146 | fungus. <span | |
1147 | class="ptmri7t-x-x-120">Plant Pathology</span>, 2015 | |
1148 | <!--l. 416--><p class="noindent" >In this work <span | |
1149 | class="ptmri7t-x-x-120">Vmatch </span>was used to cluster contigs of different assemblies into | |
1150 | groups of homologous sequences. | |
1151 | </p></li> | |
1152 | <li | |
1153 | class="enumerate" id="x1-11108x54"><a | |
1154 | id="XYAN:LU:SHE:YAN:XU:SON:2015"></a>Jun Yang, Chaolong Lu, Qi Shen, Yuying Yan, Changjiang Xu, and Chi Song. | |
1155 | The complete chloroplast genome sequence of Fagopyrum cymosum. | |
1156 | <span | |
1157 | class="ptmri7t-x-x-120">Mitochondrial DNA</span>, pages 1–2, 2015 | |
1158 | <!--l. 419--><p class="noindent" >In this work <span | |
1159 | class="ptmri7t-x-x-120">Vmatch </span>was used to identify inverted repeats in chloroplast | |
1160 | genomes. | |
1161 | </p> | |
1162 | </li></ol> | |
1163 | <!--l. 424--><p class="noindent" > | |
1164 | </p> | |
1165 | <h4 class="likesubsectionHead"><a | |
1166 | id="x1-12000"></a>Usages in the Microbial Genome Research</h4> | |
1167 | <!--l. 425--><p class="noindent" > | |
1168 | </p><ol class="enumerate1" > | |
1169 | <li | |
1170 | class="enumerate" id="x1-12002x1">The <a | |
1171 | href="http://www.llnl.gov/str/April04/Slezak.html" >KPATH system</a>, developed at the Lawrence Livermore National | |
1172 | Laboratories, and described in | |
1173 | <!--l. 432--><p class="noindent" ><a | |
1174 | id="XFIT:GAR:KUC:KUR:MYE:OTT:SLE:VIT:ZEM:MCC:2002"></a>J.P. Fitch, S.N. Gardner, T.A. Kuczmarski, S. Kurtz, R. Myers, L.L. | |
1175 | Ott, T.R. Slezak, E.A. Vitalis, A.T. Zemla, and P.M. McCready. Rapid | |
1176 | development of nucleic acid diagnostics. <span | |
1177 | class="ptmri7t-x-x-120">Proceedings of the IEEE</span>, | |
1178 | 90(11):1708–1721, 2002 | |
1179 | </p><!--l. 434--><p class="noindent" ><a | |
1180 | id="XSLE:KUC:OTT:TOR:MED:SMI:TRU:MUL:LAM:VIT:ZEM:ZHO:GAR:2003"></a>T. Slezak, T. Kuczmarski, L. Ott, C. Torres, D. Medeiros, J. Smith, | |
1181 | B. Truitt, N. Mulakken, M. Lam, E. Vitalis, A. Zemla, C.E. Zhou, and | |
1182 | S. Gardner. Comparative Genomics Tools Applied to Bioterrorism | |
1183 | Defense. <span | |
1184 | class="ptmri7t-x-x-120">Briefings in Bioinformatics</span>, 4(2):133–149, 2003 | |
1185 | ||
1186 | ||
1187 | ||
1188 | </p><!--l. 436--><p class="noindent" >used <span | |
1189 | class="ptmri7t-x-x-120">Vmatch </span>to detect unique substrings in large collection of DNA | |
1190 | sequences. These unique substrings serve as signatures allowing for rapid | |
1191 | and accurate diagnostics to identify pathogen bacteria and viruses. A | |
1192 | similar application is reported in <a | |
1193 | id="XGAR:KUC:VIT:SLE:2003"></a>S.N. Gardner, T.A. Kuczmarski, E.A. | |
1194 | Vitalis, and T.R. Slezak. Limitations of TaqMan PCR for Detecting Viral | |
1195 | Pathogens I llustrated by Hepatitis A, B, C, and E Viruses and Human | |
1196 | Immunodeficiency Virus. <span | |
1197 | class="ptmri7t-x-x-120">J.</span><span | |
1198 | class="ptmri7t-x-x-120"> of Clinical Microbiology</span>, 41(6):2417–2427, | |
1199 | 2003. | |
1200 | </p></li> | |
1201 | <li | |
1202 | class="enumerate" id="x1-12004x2"><a | |
1203 | id="XPOB:WET:SZY:SCHIL:KUR:MEY:NAT:BECK:2006"></a>N. Pobigaylo, D. Wetter, S. Szymczak, U. Schiller, S. Kurtz, F. Meyer, | |
1204 | T.W. Nattkemper, and Becker A. Construction of a large signature-tagged | |
1205 | mini-Tn5 transposon library and its application to mutagenesis of | |
1206 | <span | |
1207 | class="ptmri7t-x-x-120">Sinorhizobium meliloti</span>. <span | |
1208 | class="ptmri7t-x-x-120">Appl Environ Microbiol.</span>, 72(6):4329–4337, 2006 | |
1209 | <!--l. 444--><p class="noindent" >In this work <span | |
1210 | class="ptmri7t-x-x-120">Vmatch </span>was used to map signature tags to the genome of | |
1211 | <span | |
1212 | class="ptmri7t-x-x-120">S.</span><span | |
1213 | class="ptmri7t-x-x-120"> meliloti</span>. | |
1214 | </p></li> | |
1215 | <li | |
1216 | class="enumerate" id="x1-12006x3">The <a | |
1217 | href="http://crispr.u-psud.fr/Server/CRISPRfinder.php" >CRISPRFinder</a>-program and the <a | |
1218 | href="http://crispr.u-psud.fr/crispr/CRISPRdatabase.php" >CRISPRdatabase</a>, described in | |
1219 | <!--l. 452--><p class="noindent" ><a | |
1220 | id="XGRI:VER:POU:2007A"></a>I. Grissa, G. Vergnaud, and C. Pourcel. CRISPRFinder: a web tool to | |
1221 | identify clustered regularly interspaced short palindromic repeats. <span | |
1222 | class="ptmri7t-x-x-120">Nucleic</span> | |
1223 | <span | |
1224 | class="ptmri7t-x-x-120">Acids Res</span>, 35(Web Server issue):W52–7, 2007 | |
1225 | </p><!--l. 454--><p class="noindent" ><a | |
1226 | id="XGRI:VER:POU:2007B"></a>I. Grissa, G. Vergnaud, and C. Pourcel. The CRISPRdb database and tools | |
1227 | to display CRISPRs and to generate dictionaries of spacers and repeats. | |
1228 | <span | |
1229 | class="ptmri7t-x-x-120">BMC Bioinformatics</span>, 8:172, 2007 | |
1230 | </p><!--l. 456--><p class="noindent" >used <span | |
1231 | class="ptmri7t-x-x-120">Vmatch </span>to efficiently find maximal repeats, as a first step in localizing | |
1232 | Clustered regularly interspaced short palindromic repeats (CRISPRs). | |
1233 | </p></li> | |
1234 | <li | |
1235 | class="enumerate" id="x1-12008x4"><a | |
1236 | id="XVOSS:GEO:SCHOE:UDE:HES:2009"></a>B. Voss, J. Georg, V. Schöon, S. Ude, and W. R. Hess. Biocomputational | |
1237 | prediction of non-coding RNAs in model cyanobacteria. <span | |
1238 | class="ptmri7t-x-x-120">BMC Genomics</span>, | |
1239 | 10:123, 2009 | |
1240 | <!--l. 462--><p class="noindent" >In this work <span | |
1241 | class="ptmri7t-x-x-120">Vmatch </span>was used to map predicted sequences to information | |
1242 | about Rho-independent terminators provided by a specific database. | |
1243 | </p></li> | |
1244 | <li | |
1245 | class="enumerate" id="x1-12010x5"><a | |
1246 | id="XSCHMU:CAN:SCHLU:MA:MIT:NEL:HYT:SON:THE:CHE:2010"></a>Jeremy Schmutz, Steven B Cannon, Jessica Schlueter, Jianxin Ma, Therese | |
1247 | ||
1248 | ||
1249 | ||
1250 | Mitros, William Nelson, David L Hyten, Qijian Song, Jay J Thelen, Jianlin | |
1251 | Cheng, et al. Genome sequence of the palaeopolyploid soybean. <span | |
1252 | class="ptmri7t-x-x-120">Nature</span>, | |
1253 | 463(7278):178–183, 2010 | |
1254 | <!--l. 466--><p class="noindent" >In this work <span | |
1255 | class="ptmri7t-x-x-120">Vmatch </span>was used to cluster DNA-sequences into families based | |
1256 | on their six-frame translation. | |
1257 | </p></li> | |
1258 | <li | |
1259 | class="enumerate" id="x1-12012x6"><a | |
1260 | id="XZIM:GES:CHE:LOR:SCHRO:2010"></a>Bob Zimmermann, Tanja Gesell, Doris Chen, Christina Lorenz, Renée | |
1261 | Schroeder, and J Valcarcel. Monitoring genomic sequences during selex | |
1262 | using high-throughput sequencing: neutral selex. <span | |
1263 | class="ptmri7t-x-x-120">PLoS One</span>, 5(2):e9169, | |
1264 | 2010 | |
1265 | <!--l. 469--><p class="noindent" >In this work <span | |
1266 | class="ptmri7t-x-x-120">Vmatch </span>was used to align 454-sequences to the Ecoli-genome | |
1267 | and to cluster the sequences. | |
1268 | </p></li> | |
1269 | <li | |
1270 | class="enumerate" id="x1-12014x7"><a | |
1271 | id="XTOU:DEN:MED:BAR:ELK:PET:2010"></a>Fabrice Touzain, Erick Denamur, Claudine Médigue, Valérie Barbe, | |
1272 | Meriem El Karoui, Marie-Agnès Petit, et al. Small variable segments | |
1273 | constitute a major type of diversity of bacterial genomes at the species level. | |
1274 | <span | |
1275 | class="ptmri7t-x-x-120">Genome Biol</span>, 11(4):R45, 2010 | |
1276 | <!--l. 472--><p class="noindent" >In this work <span | |
1277 | class="ptmri7t-x-x-120">Vmatch </span>was used for detecting repeats in three bacterial | |
1278 | species. | |
1279 | </p></li> | |
1280 | <li | |
1281 | class="enumerate" id="x1-12016x8"><a | |
1282 | id="XMAY:MAR:HED:SIM:LIU:MOR:STEU:TAU:ROE:GUN:2011"></a>Klaus FX Mayer, Mihaela Martis, Pete E Hedley, Hana Šimková, Hui Liu, | |
1283 | Jenny A Morris, Burkhard Steuernagel, Stefan Taudien, Stephan Roessner, | |
1284 | Heidrun Gundlach, et al. Unlocking the barley genome by chromosomal | |
1285 | and comparative genomics. <span | |
1286 | class="ptmri7t-x-x-120">The Plant Cell</span>, 23(4):1249–1263, 2011 | |
1287 | <!--l. 475--><p class="noindent" >In this work <span | |
1288 | class="ptmri7t-x-x-120">Vmatch </span>was used for masking repeats in 454-reads. | |
1289 | </p></li> | |
1290 | <li | |
1291 | class="enumerate" id="x1-12018x9"><a | |
1292 | id="XPUS:MAN:JI:LI:EVA:CRA:MOR:MEA:SIN:SAX:2011"></a>Smruti Pushalkar, Shrinivasrao P Mane, Xiaojie Ji, Yihong Li, Clive Evans, | |
1293 | Oswald R Crasta, Douglas Morse, Robert Meagher, Anup Singh, and | |
1294 | Deepak Saxena. Microbial diversity in saliva of oral squamous cell | |
1295 | carcinoma. <span | |
1296 | class="ptmri7t-x-x-120">FEMS Immunology & Medical Microbiology</span>, 61(3):269–277, | |
1297 | 2011 | |
1298 | <!--l. 478--><p class="noindent" >In this work <span | |
1299 | class="ptmri7t-x-x-120">Vmatch </span>was used to identify distal primers. | |
1300 | ||
1301 | ||
1302 | ||
1303 | </p></li> | |
1304 | <li | |
1305 | class="enumerate" id="x1-12020x10"><a | |
1306 | id="XBRE:SHE:POP:2011"></a>J. E. Breitenbach, K. S. Shelby, and H. JR Popham. Baculovirus induced | |
1307 | transcripts in hemocytes from the larvae of heliothis virescens. <span | |
1308 | class="ptmri7t-x-x-120">Viruses</span>, | |
1309 | 3(11):2047–2064, 2011 | |
1310 | <!--l. 483--><p class="noindent" >In this work <span | |
1311 | class="ptmri7t-x-x-120">Vmatch </span>was used for removing redundant transcripts | |
1312 | assembled in an RNA-seq study based on Illumina reads for <span | |
1313 | class="ptmri7t-x-x-120">Heliothis</span> | |
1314 | <span | |
1315 | class="ptmri7t-x-x-120">virescens </span>(tobacco budworm), infected with a virus. | |
1316 | </p></li> | |
1317 | <li | |
1318 | class="enumerate" id="x1-12022x11"><a | |
1319 | id="XTRI:HAM:BUE:TIS:VER:ZIN:LEA:2011"></a>LR Triplett, JP Hamilton, CR Buell, NA Tisserat, V. Verdier, F Zink, | |
1320 | and JE Leach. Genomic analysis of xanthomonas oryzae isolates from | |
1321 | rice grown in the united states reveals substantial divergence from | |
1322 | known x. oryzae pathovars. <span | |
1323 | class="ptmri7t-x-x-120">Applied and Environmental Microbiology</span>, | |
1324 | 77(12):3930–3937, 2011 | |
1325 | <!--l. 488--><p class="noindent" >In this work <span | |
1326 | class="ptmri7t-x-x-120">Vmatch </span>was used to search unassembled Illumina reads of US | |
1327 | and African strains of <span | |
1328 | class="ptmri7t-x-x-120">Xanthomonas oryzae </span>for evidence of transcriptional | |
1329 | activator-like effector sequences. | |
1330 | </p></li> | |
1331 | <li | |
1332 | class="enumerate" id="x1-12024x12"><span | |
1333 | class="ptmri7t-x-x-120">Vmatch </span>is used as an integral part of the PriMUX software package | |
1334 | described in | |
1335 | <!--l. 493--><p class="noindent" ><a | |
1336 | id="XHYS:NAR:ELS:CAR:WIL:GAR:2012"></a>D. A. Hysom, P. Naraghi-Arani, M. Elsheikh, A. C. Carrillo, P. L. | |
1337 | Williams, and S. N. Gardner. Skip the alignment: degenerate, multiplex | |
1338 | primer and probe design using K-mer matching instead of alignments. <span | |
1339 | class="ptmri7t-x-x-120">PLoS</span> | |
1340 | <span | |
1341 | class="ptmri7t-x-x-120">ONE</span>, 7(4):e34560, 2012 | |
1342 | </p><!--l. 495--><p class="noindent" >In this context <span | |
1343 | class="ptmri7t-x-x-120">Vmatch </span>used for selecting multiplex compatible, degenerate | |
1344 | primers and probes to detect diverse targets such as viruses. | |
1345 | </p></li> | |
1346 | <li | |
1347 | class="enumerate" id="x1-12026x13"><a | |
1348 | id="XSHE:POP:2012"></a>K. S. Shelby and H. JR Popham. Rna-seq study of microbially | |
1349 | induced hemocyte transcripts from larval heliothis virescens (lepidoptera: | |
1350 | Noctuidae). <span | |
1351 | class="ptmri7t-x-x-120">Insects</span>, 3(3):743–762, 2012 | |
1352 | <!--l. 499--><p class="noindent" >In this work <span | |
1353 | class="ptmri7t-x-x-120">Vmatch </span>was used to identify redundant contigs from de novo | |
1354 | exome assemblies. | |
1355 | </p></li> | |
1356 | <li | |
1357 | class="enumerate" id="x1-12028x14"><a | |
1358 | id="XHUR:SUL:2013"></a>B. L. Hurwitz and M. B. Sullivan. The Pacific Ocean virome (POV): | |
1359 | ||
1360 | ||
1361 | ||
1362 | a marine viral metagenomic dataset and associated protein clusters for | |
1363 | quantitative viral ecology. <span | |
1364 | class="ptmri7t-x-x-120">PLoS ONE</span>, 8(2):e57355, 2013 | |
1365 | <!--l. 503--><p class="noindent" >In this work <span | |
1366 | class="ptmri7t-x-x-120">Vmatch </span>was used to identify reads which have no common | |
1367 | 20-mers with other reads in a context of a marine viral metagenome project. | |
1368 | </p></li> | |
1369 | <li | |
1370 | class="enumerate" id="x1-12030x15"><a | |
1371 | id="XZHU:RHO:FESCH:2013"></a>X. Zhuo, M. Rho, and C. Feschotte. Genome-wide characterization of | |
1372 | endogenous retroviruses in the bat Myotis lucifugus reveals recent and | |
1373 | diverse infections. <span | |
1374 | class="ptmri7t-x-x-120">J. Virol.</span>, 87(15):8493–8501, Aug 2013 | |
1375 | <!--l. 507--><p class="noindent" >In this work <span | |
1376 | class="ptmri7t-x-x-120">Vmatch </span>was used for clustering potential complete Endogenous | |
1377 | retroviruses of the bat <span | |
1378 | class="ptmri7t-x-x-120">Myotis lucifugus </span>into subfamilies. | |
1379 | </p></li> | |
1380 | <li | |
1381 | class="enumerate" id="x1-12032x16">In the three papers | |
1382 | <!--l. 511--><p class="noindent" ><a | |
1383 | id="XHUR:WES:BRU:SUL:2014"></a>B. L. Hurwitz, A. H. Westveld, J. R. Brum, and M. B. Sullivan. | |
1384 | Modeling ecological drivers in marine viral communities using comparative | |
1385 | metagenomics and network analyses. <span | |
1386 | class="ptmri7t-x-x-120">Proc. Natl. Acad. Sci. U.S.A.</span>, | |
1387 | 111(29):10714–10719, July 2014 | |
1388 | </p><!--l. 513--><p class="noindent" ><a | |
1389 | id="XHUR:DEN:POU:SUL:2013"></a>B. L. Hurwitz, L. Deng, B. T. Poulos, and M. B. Sullivan. Evaluation | |
1390 | of methods to concentrate and purify ocean virus communities | |
1391 | through comparative, replicated metagenomics. <span | |
1392 | class="ptmri7t-x-x-120">Environ. Microbiol.</span>, | |
1393 | 15(5):1428–1440, May 2013 | |
1394 | </p><!--l. 515--><p class="noindent" ><a | |
1395 | id="XBRU:HUR:SCHOF:DUC:SUL:2015"></a>J. R. Brum, B. L. Hurwitz, O. Schofield, H. W. Ducklow, and M. B. | |
1396 | Sullivan. Seasonal time bombs: dominant temperate viruses affect southern | |
1397 | ocean microbial dynamics. <span | |
1398 | class="ptmri7t-x-x-120">The ISME journal</span>, 2015 | |
1399 | </p><!--l. 517--><p class="noindent" ><span | |
1400 | class="ptmri7t-x-x-120">Vmatch </span>was used for <span | |
1401 | class="zptmcm7m-x-x-120">k</span>-mer analysis in the context of different marine | |
1402 | metagenome projects. | |
1403 | </p></li> | |
1404 | <li | |
1405 | class="enumerate" id="x1-12034x17"><a | |
1406 | id="XDEC:PAR:2014"></a>C. J. Decker and R. Parker. Analysis of double-stranded rna from | |
1407 | microbial communities identifies double-stranded rna virus-like elements. | |
1408 | <span | |
1409 | class="ptmri7t-x-x-120">Cell reports</span>, 7(3):898–906, 2014 | |
1410 | <!--l. 521--><p class="noindent" >In this work <span | |
1411 | class="ptmri7t-x-x-120">Vmatch </span>was used for <span | |
1412 | class="zptmcm7m-x-x-120">k</span>-mer analysis in the context of microbial | |
1413 | communities. | |
1414 | </p></li> | |
1415 | <li | |
1416 | class="enumerate" id="x1-12036x18"><a | |
1417 | id="XBEN:BOU:FIC:KRI:LAR:2014"></a>J. Bengtsson-Palme, F. Boulund, J. Fick, E. Kristiansson, and D. G. | |
1418 | ||
1419 | ||
1420 | ||
1421 | Larsson. Shotgun metagenomics reveals a wide array of antibiotic | |
1422 | resistance genes and mobile elements in a polluted lake in India. <span | |
1423 | class="ptmri7t-x-x-120">Front</span> | |
1424 | <span | |
1425 | class="ptmri7t-x-x-120">Microbiol</span>, 5:648, 2014 | |
1426 | <!--l. 525--><p class="noindent" >In this work <span | |
1427 | class="ptmri7t-x-x-120">Vmatch </span>was used in an iterative scheme to construct contigs | |
1428 | from reads associated with resistance genes in the context of a shotgun | |
1429 | metagenome project. | |
1430 | </p></li> | |
1431 | <li | |
1432 | class="enumerate" id="x1-12038x19"><a | |
1433 | id="XNIC:THI:GAR:MCL:FOF:KOS:ELL:BRE:JAC:JAI:2013"></a>A Be Nicholas, James B Thissen, Shea N Gardner, Kevin S McLoughlin, | |
1434 | Viacheslav Y Fofanov, Heather Koshinsky, Sally R Ellingson, Thomas S | |
1435 | Brettin, Paul J Jackson, and Crystal J Jaing. Detection of <span | |
1436 | class="ptmri7t-x-x-120">Bacillus</span> | |
1437 | <span | |
1438 | class="ptmri7t-x-x-120">anthracis </span>DNA in complex soil and air samples using next-generation | |
1439 | sequencing. <span | |
1440 | class="ptmri7t-x-x-120">PloS one</span>, 8(9), 2013 | |
1441 | <!--l. 529--><p class="noindent" >In this work <span | |
1442 | class="ptmri7t-x-x-120">Vmatch </span>was used to match probe candidate sequences against | |
1443 | viral sequences and the human genmome sequence. | |
1444 | </p></li> | |
1445 | <li | |
1446 | class="enumerate" id="x1-12040x20"><a | |
1447 | id="XHEN:RUM:SCZ:VEL:DIE:GER:GOM:RAH:STO:BOR:2014"></a>Birgit Henrich, Madis Rumming, Alexander Sczyrba, Eunike Velleuer, Ralf | |
1448 | Dietrich, Wolfgang Gerlach, Michael Gombert, Sebastian Rahn, Jens Stoye, | |
1449 | Arndt Borkhardt, et al. <span | |
1450 | class="ptmri7t-x-x-120">Mycoplasma salivarium </span>as a dominant coloniser of | |
1451 | <span | |
1452 | class="ptmri7t-x-x-120">Fanconi anaemia </span>associated oral carcinoma. <span | |
1453 | class="ptmri7t-x-x-120">PloS one</span>, 9(3), 2014 | |
1454 | <!--l. 533--><p class="noindent" >In this work <span | |
1455 | class="ptmri7t-x-x-120">Vmatch </span>was used to identify the species of the | |
1456 | Streptococcaceae by comparing with Silva 115 release 16S reference | |
1457 | sequence database.</p></li></ol> | |
1458 | <!--l. 537--><p class="noindent" > | |
1459 | </p> | |
1460 | <h4 class="likesubsectionHead"><a | |
1461 | id="x1-13000"></a>Usages in General Web-Servers or Sequence Analysis Software</h4> | |
1462 | <!--l. 538--><p class="noindent" > | |
1463 | </p><ol class="enumerate1" > | |
1464 | <li | |
1465 | class="enumerate" id="x1-13002x1">Since 2000, the <a | |
1466 | href="http://rsat.ulb.ac.be/rsat/" >RSA-tools</a>, described in | |
1467 | <!--l. 543--><p class="noindent" ><a | |
1468 | id="XHEL:RIO:COL:2000"></a>J. van Helden, A.F. Rios, and J. Collado-Vides. Discovering Regulatory | |
1469 | Elements in Non-Coding Sequences by Analysis of Spaced Dyads. <span | |
1470 | class="ptmri7t-x-x-120">Nucleic</span> | |
1471 | ||
1472 | ||
1473 | ||
1474 | <span | |
1475 | class="ptmri7t-x-x-120">Acids Res.</span>, 28(8):1808–1818, 2000 | |
1476 | </p><!--l. 545--><p class="noindent" >and developed by Jacques van Helden use <span | |
1477 | class="ptmri7t-x-x-120">Vmatch </span>to <a | |
1478 | href="http://rsat.ulb.ac.be/rsat/purge-sequence_form.cgi" >purge</a> sequences | |
1479 | before computing sequence statistics. Similar applications are reported in | |
1480 | the following papers: | |
1481 | </p><!--l. 550--><p class="noindent" ><a | |
1482 | id="XHUL:WEE:CRO:GER:HEP:HEL:2003"></a>R.J.M. Hulzink, H. Weerdesteyn, A.F. Croes, M.M.A. Gerats, T. van | |
1483 | Herpen, and J. van Helden. In Silico Identification of Putative Regulatory | |
1484 | Sequence Elements in the 5’-Untranslated Region of Genes That Are | |
1485 | Expressed during Male Gametogenesis Gene Co-regulation. <span | |
1486 | class="ptmri7t-x-x-120">Plant Physiol.</span>, | |
1487 | 132:75–83, 2003 | |
1488 | </p><!--l. 552--><p class="noindent" ><a | |
1489 | id="XSIM:WOD:COH:HEL:2004"></a>N. Simonis, S.J. Wodak, G.N. Cohen, and | |
1490 | J van Helden. Combining Pattern Discovery and Discriminant Analysis to | |
1491 | Predict Gene Co-regulation. <span | |
1492 | class="ptmri7t-x-x-120">Bioinformatics</span>, 20:2370–2379, 2004 | |
1493 | </p><!--l. 554--><p class="noindent" ><a | |
1494 | id="XSIM:HEL:COH:WOD:2004"></a>N. Simonis, J. van Helden, G.N. Cohen, and S.J. Wodak. Transcriptional | |
1495 | regulation of protein complexes in yeast. <span | |
1496 | class="ptmri7t-x-x-120">Genome Biology</span>, 5:R33, 2004. | |
1497 | </p></li> | |
1498 | <li | |
1499 | class="enumerate" id="x1-13004x2">The program <a | |
1500 | href="http://splicenest.molgen.mpg.de/" >SpliceNest</a>, described in | |
1501 | <!--l. 559--><p class="noindent" ><a | |
1502 | id="XCOW:HAA:VIN:2002"></a>E. Coward, S.A. Haas, and M. Vingron. SpliceNest: Visualization of Gene | |
1503 | Structure and Alternative Splicing Based on EST Clusters. <span | |
1504 | class="ptmri7t-x-x-120">Trends Genet.</span>, | |
1505 | 18(1):53–55, 2002 | |
1506 | </p><!--l. 561--><p class="noindent" >computes gene indices and uses <span | |
1507 | class="ptmri7t-x-x-120">Vmatch </span>to <a | |
1508 | href="http://splicenest.molgen.mpg.de/doc/help.html#mapping" >map</a> clustered sequences to large | |
1509 | genomes. | |
1510 | </p></li> | |
1511 | <li | |
1512 | class="enumerate" id="x1-13006x3"><a | |
1513 | href="http://bibiserv.techfak.uni-bielefeld.de/e2g/" >e2g</a> is a web-based server which efficiently maps large EST and cDNA data | |
1514 | sets to genomic DNA. The use of <span | |
1515 | class="ptmri7t-x-x-120">Vmatch </span>allows to significantly extend the | |
1516 | size of data that can be mapped in reasonable time. e2g is available as a | |
1517 | web service and hosts large collections of EST sequences (e.g. 4.1 million | |
1518 | mouse ESTs of 1.87 Gbp) in a precomputed persistent index. For details see | |
1519 | <!--l. 579--><p class="noindent" ><a | |
1520 | id="XKRUE:SCZ:KUR:GIE:2004"></a>J. Krüger, A. Sczyrba, S. Kurtz, and R. Giegerich. e2g: An interactive | |
1521 | web-based server for efficiently mapping large EST and cDNA sets to | |
1522 | genomic sequences. <span | |
1523 | class="ptmri7t-x-x-120">Nucleic Acids Res.</span>, 32:W301–W304, 2004. | |
1524 | </p></li> | |
1525 | <li | |
1526 | class="enumerate" id="x1-13008x4">The <a | |
1527 | href="http://bibiserv.techfak.uni-bielefeld.de/" >Bielefeld Bioinformatics Server</a> provides the <a | |
1528 | href="http://bibiserv.techfak.uni-bielefeld.de/reputer/" >REPuter</a> web-service to | |
1529 | compute repeats in complete genomes. The service is based on <span | |
1530 | class="ptmri7t-x-x-120">Vmatch</span>. | |
1531 | ||
1532 | ||
1533 | ||
1534 | </li> | |
1535 | <li | |
1536 | class="enumerate" id="x1-13010x5"><a | |
1537 | id="XFER:DON:SCHNE:MOR:NAN:BRE:WAL:2004"></a>J. Fernandes, Q. Dong, B. Schneider, D.J. Morrow, | |
1538 | G.-L. Nan, V. Brendel, and V. Walbot. Genome-wide mutagenesis of Zea | |
1539 | mays L. using RescueMu transposons. <span | |
1540 | class="ptmri7t-x-x-120">Genome Biology</span>, 5(10):R82, 2004 | |
1541 | <!--l. 589--><p class="noindent" >In this work <span | |
1542 | class="ptmri7t-x-x-120">Vmatch </span>was used to (1) match 130 861 vector-trimmed | |
1543 | sequences against the maize repeat database, and (2) to cluster | |
1544 | near-identical sequences. | |
1545 | </p></li> | |
1546 | <li | |
1547 | class="enumerate" id="x1-13012x6"><a | |
1548 | href="http://www-ab.informatik.uni-tuebingen.de/software/crosslink/welcome.html" >CrossLink</a>, described in | |
1549 | <!--l. 595--><p class="noindent" ><a | |
1550 | id="XDEZ:SCHAEF:WIE:WEI:HUS:2006"></a>T. Dezulian, M. Schaefer, R. Wiese, D. Weigel, and D.H. Huson. | |
1551 | CrossLink: visualization and exploration of sequence relationships between | |
1552 | (micro) RNAs. <span | |
1553 | class="ptmri7t-x-x-120">Nucleic Acids Res.</span>, 34(Web Server Issue):W400–W404, | |
1554 | 200 | |
1555 | </p><!--l. 597--><p class="noindent" >is a versatile computational tool which aids in visualizing relationships | |
1556 | between RNA sequences (particularly between ncRNAs and their putative | |
1557 | target transcripts) in an intuitive and accessible way. Besides BLAST, | |
1558 | CrossLink uses <span | |
1559 | class="ptmri7t-x-x-120">Vmatch </span>to reveal the sequence relationships to be visualized. | |
1560 | </p></li> | |
1561 | <li | |
1562 | class="enumerate" id="x1-13014x7">The early version of the web-service <a | |
1563 | href="http://mips.gsf.de/simap/" >Similarity matrix of Proteins (SIMAP)</a>, | |
1564 | see | |
1565 | <!--l. 607--><p class="noindent" ><a | |
1566 | id="XARN:RAT:TIS:TRU:STU:MEW:2005"></a>R. Arnold, T. Rattei, P. Tischler, M.-D. Truong, V. Stümpflen, and H.W. | |
1567 | Mewes. SIMAP - The similarity matrix of proteins. <span | |
1568 | class="ptmri7t-x-x-120">Bioinformatics</span>, | |
1569 | 21(Suppl. 2):ii42–ii46, 2005 | |
1570 | </p><!--l. 609--><p class="noindent" >used <span | |
1571 | class="ptmri7t-x-x-120">Vmatch </span>to locate the sequences in SIMAP which are similar to a given | |
1572 | query. This is much faster than running BLAST. | |
1573 | </p></li> | |
1574 | <li | |
1575 | class="enumerate" id="x1-13016x8"><a | |
1576 | id="XFIE:VAN:PEE:VAN:NAP:2005"></a>Fiers, M.W.E.J. and Van de Wetering, H. and Peeters, T.H.J.M. and van | |
1577 | Wijk, J.J. and Nap, J-P. DNAVis: interactive visualization of comparative | |
1578 | genome annotations. <span | |
1579 | class="ptmri7t-x-x-120">Bioinformatics</span>, 22(3):354–355, 2005 | |
1580 | <!--l. 615--><p class="noindent" >In this work <span | |
1581 | class="ptmri7t-x-x-120">Vmatch </span>was used to compute similarities between genomes, | |
1582 | which are then visualized by the program <a | |
1583 | href="http://www.win.tue.nl/dnavis/" >DNAVis</a>. | |
1584 | </p></li> | |
1585 | <li | |
1586 | class="enumerate" id="x1-13018x9">In the paper | |
1587 | ||
1588 | ||
1589 | ||
1590 | <!--l. 619--><p class="noindent" ><a | |
1591 | id="XSEI:KRUE:HAR:SCHWA:LOEW:MER:DAN:GIE:2006"></a>P.N. Seibel, J. Krüger, S. Hartmeier, K. Schwarzer, K. Löwenthal, | |
1592 | H. Mersch, T. Dandekar, and R. Giegerich. XML schemas for common | |
1593 | bioinformatic data types and their application in workflow systems. <span | |
1594 | class="ptmri7t-x-x-120">BMC</span> | |
1595 | <span | |
1596 | class="ptmri7t-x-x-120">Bioinformatics</span>, 7:490, 2006 | |
1597 | </p><!--l. 621--><p class="noindent" >Seidel et. al. describe methods for creating web-services and give | |
1598 | examples which, among other tools, also integrate <span | |
1599 | class="ptmri7t-x-x-120">Vmatch</span>. | |
1600 | </p></li> | |
1601 | <li | |
1602 | class="enumerate" id="x1-13020x10">The program <span | |
1603 | class="ptmri7t-x-x-120">Gepard</span> | |
1604 | <!--l. 628--><p class="noindent" ><a | |
1605 | id="XKRU:ARN:RAT:2007"></a>J. Krumsiek, R. Arnold, and T. Rattei. Gepard: a rapid and sensitive tool | |
1606 | for creating dotplots on genome scale. <span | |
1607 | class="ptmri7t-x-x-120">Bioinformatics</span>, 23(8):1026–8, 2007 | |
1608 | </p><!--l. 630--><p class="noindent" >uses <span | |
1609 | class="ptmri7t-x-x-120">mkvtree </span>to compute enhanced suffix arrays. | |
1610 | </p></li> | |
1611 | <li | |
1612 | class="enumerate" id="x1-13022x11"><span | |
1613 | class="ptmri7t-x-x-120">Vmatch </span>is used a part of the transcriptome assembler software Rnnotator, | |
1614 | described in | |
1615 | <!--l. 636--><p class="noindent" ><a | |
1616 | id="XMAR:BRU:FAN:MEN:BLO:ZHA:SHE:SNY:WAN:2010"></a>J. Martin, V. M. Bruno, Z. Fang, X. Meng, M. Blow, T. Zhang, | |
1617 | G. Sherlock, M. Snyder, and Z. Wang. Rnnotator: an automated de novo | |
1618 | transcriptome assembly pipeline from stranded RNA-Seq reads. <span | |
1619 | class="ptmri7t-x-x-120">BMC</span> | |
1620 | <span | |
1621 | class="ptmri7t-x-x-120">Genomics</span>, 11:663, 2010 | |
1622 | </p></li> | |
1623 | <li | |
1624 | class="enumerate" id="x1-13024x12">The BioExtract-Server described in | |
1625 | <!--l. 640--><p class="noindent" ><a | |
1626 | id="XLUS:JEN:BRE:2011"></a>C. M. Lushbough, D. M. Jennewein, and V. Brendel. The bioextract | |
1627 | server: a web-based bioinformatic workflow platform. <span | |
1628 | class="ptmri7t-x-x-120">Nucleic acids</span> | |
1629 | <span | |
1630 | class="ptmri7t-x-x-120">research</span>, 39(suppl 2):W528–W532, 2011 | |
1631 | </p><!--l. 642--><p class="noindent" >uses <span | |
1632 | class="ptmri7t-x-x-120">Vmatch </span>to remove duplicated sequences. | |
1633 | </p></li> | |
1634 | <li | |
1635 | class="enumerate" id="x1-13026x13"><a | |
1636 | id="XLUS:GNI:DOO:2015"></a>C. M. Lushbough, E. Z. Gnimpieba, and R. Dooley. Life science data | |
1637 | analysis workflow development using the bioextract server leveraging the | |
1638 | iplant collaborative cyberinfrastructure. <span | |
1639 | class="ptmri7t-x-x-120">Concurrency and Computation:</span> | |
1640 | <span | |
1641 | class="ptmri7t-x-x-120">Practice and Experience</span>, 27(2):408–419, 2015 | |
1642 | <!--l. 648--><p class="noindent" >In this work <span | |
1643 | class="ptmri7t-x-x-120">Vmatch </span>was used for removing duplicates in BlastP results. | |
1644 | This use is part of a workflow in <a | |
1645 | href="http://www.myexperiment.org/workflows/3131.html" >myexperiment</a>. | |
1646 | ||
1647 | ||
1648 | ||
1649 | </p></li> | |
1650 | <li | |
1651 | class="enumerate" id="x1-13028x14"><a | |
1652 | id="XGRE:LOY:HOR:RAT:2015"></a>Daniel Greuter, Alexander Loy, Matthias Horn, and Thomas Rattei. | |
1653 | ProbeBase-an online resource for rRNA-targeted oligonucleotide probes | |
1654 | and primers: new features 2016. <span | |
1655 | class="ptmri7t-x-x-120">Nucleic acids research</span>, page gkv1232, | |
1656 | 2015 | |
1657 | <!--l. 651--><p class="noindent" >In this work <span | |
1658 | class="ptmri7t-x-x-120">Vmatch </span>was used for probe/primer search functionality in the | |
1659 | probeBase database.</p></li></ol> | |
1660 | <!--l. 655--><p class="noindent" > | |
1661 | </p> | |
1662 | <h4 class="likesubsectionHead"><a | |
1663 | id="x1-14000"></a>Current Usages in Human Genome Research</h4> | |
1664 | <!--l. 656--><p class="noindent" > | |
1665 | </p><ol class="enumerate1" > | |
1666 | <li | |
1667 | class="enumerate" id="x1-14002x1"><a | |
1668 | id="XBUC:JAR:MEN:MAT:SCO:GRE:LAN:DUM:2005"></a>P.G. Buckley, C. Jarbo, U. Menzel, T. Mathiesen, C. Scott, S.G. Gregory, | |
1669 | C.F. Langford, and J.P. Dumanski. Comprehensive DNA Copy Number | |
1670 | Profiling of Meningioma Using a Chromosome 1 Tiling Path Microarray | |
1671 | identifies Novel Candidate Tumor Surpressor Loci. <span | |
1672 | class="ptmri7t-x-x-120">Cancer Res.</span>, | |
1673 | 65(7):2653–2661, 2005 | |
1674 | <!--l. 659--><p class="noindent" >In this work <span | |
1675 | class="ptmri7t-x-x-120">Vmatch </span>was used to reveal long repeats inside human | |
1676 | chromosome 1 and long similar regions between human chromosome 1 and | |
1677 | all other human chromosomes. | |
1678 | </p></li> | |
1679 | <li | |
1680 | class="enumerate" id="x1-14004x2"><a | |
1681 | id="XLIA:WAN:LIU:JI:LIU:CHE:WEB:REE:DEA:2007"></a>Liang, C. and Wang, G. and Liu, L. and Ji, G. and Liu, Y. and Chen, J. and | |
1682 | Webb, J.S. and Reese, G. and Dean, J.F.D. WebTraceMiner: a web service | |
1683 | for processing and mining EST sequence trace files. <span | |
1684 | class="ptmri7t-x-x-120">Nucleic Acids Res</span>, | |
1685 | 35(Web Server issue):W137–42, 2007 | |
1686 | <!--l. 662--><p class="noindent" >In this work <span | |
1687 | class="ptmri7t-x-x-120">Vmatch </span>was used for Vector screening. | |
1688 | </p></li> | |
1689 | <li | |
1690 | class="enumerate" id="x1-14006x3"><a | |
1691 | id="XNYG:JAC:LIN:ERI:BAL:FLY:TOL:MOE:SOE:KRO:LIT:2009"></a>Sanne Nygaard, Anders Jacobsen, Morten Lindow, Jens Eriksen, Eva | |
1692 | Balslev, Henrik Flyger, Niels Tolstrup, Søren Møller, Anders Krogh, and | |
1693 | Thomas Litman. Identification and analysis of mirnas in human breast | |
1694 | ||
1695 | ||
1696 | ||
1697 | cancer and teratoma samples using deep sequencing. <span | |
1698 | class="ptmri7t-x-x-120">BMC Medical</span> | |
1699 | <span | |
1700 | class="ptmri7t-x-x-120">Genomics</span>, 2(1):35, 2009 | |
1701 | <!--l. 665--><p class="noindent" >In this work <span | |
1702 | class="ptmri7t-x-x-120">Vmatch </span>was used for mapping short reads. | |
1703 | </p></li> | |
1704 | <li | |
1705 | class="enumerate" id="x1-14008x4"><a | |
1706 | id="XCOL:SOB:LU:THA:BOW:BRO:GRE:BAR:HUT:2009"></a>Christian Cole, Andrew Sobala, Cheng Lu, Shawn R Thatcher, Andrew | |
1707 | Bowman, John WS Brown, Pamela J Green, Geoffrey J Barton, and | |
1708 | Gyorgy Hutvagner. Filtering of deep sequencing data reveals the | |
1709 | existence of abundant dicer-dependent small rnas derived from trnas. <span | |
1710 | class="ptmri7t-x-x-120">Rna</span>, | |
1711 | 15(12):2147–2160, 2009 | |
1712 | <!--l. 668--><p class="noindent" >In this work <span | |
1713 | class="ptmri7t-x-x-120">Vmatch </span>was used for matching reads to sets of RNA sequences | |
1714 | and the Human genome. | |
1715 | </p></li> | |
1716 | <li | |
1717 | class="enumerate" id="x1-14010x5"><a | |
1718 | id="XCLO:WAN:XU:GU:LEA:HEA:BAR:STE:MAR:NOU:2011"></a>N. Cloonan, S. Wani, Q. Xu, J. Gu, K. Lea, S. Heater, C. Barbacioru, | |
1719 | A. L. Steptoe, H. C. Martin, E. Nourbakhsh, et al. Micrornas and their | |
1720 | isomirs function cooperatively to target common biological pathways. | |
1721 | <span | |
1722 | class="ptmri7t-x-x-120">Genome Biol</span>, 12(12):R126, 2011 | |
1723 | <!--l. 671--><p class="noindent" >In this work <span | |
1724 | class="ptmri7t-x-x-120">Vmatch </span>was used to uniquely map miRNAs against the human | |
1725 | genome. | |
1726 | </p></li> | |
1727 | <li | |
1728 | class="enumerate" id="x1-14012x6"><a | |
1729 | id="XTAK:TSU:KAT:OKA:HOR:IKE:URA:KAW:HAS:IKE:2011"></a>K Takayama, S Tsutsumi, S Katayama, T Okayama, K Horie-Inoue, | |
1730 | K Ikeda, T Urano, C Kawazu, A Hasegawa, K Ikeo, et al. Integration | |
1731 | of cap analysis of gene expression and chromatin immunoprecipitation | |
1732 | analysis on array reveals genome-wide androgen receptor signaling in | |
1733 | prostate cancer cells. <span | |
1734 | class="ptmri7t-x-x-120">Oncogene</span>, 30(5):619–630, 2011 | |
1735 | <!--l. 674--><p class="noindent" >In this work <span | |
1736 | class="ptmri7t-x-x-120">Vmatch </span>was used to determine the positions of CAGE tags on | |
1737 | the human genome. | |
1738 | </p></li> | |
1739 | <li | |
1740 | class="enumerate" id="x1-14014x7"><a | |
1741 | id="XKEV:LAL:LI:CAV:NAR:KAM:MIT:HAK:KOZ:GEN:2011"></a>Kevin CH Ha, Emilie Lalonde, Lili Li, Luca Cavallone, Rachael Natrajan, | |
1742 | Maryou B Lambros, Costas Mitsopoulos, Jarle Hakas, Iwanka Kozarewa, | |
1743 | Kerry Fenwick, et al. Identification of gene fusion transcripts by | |
1744 | transcriptome sequencing in BRCA1-mutated breast cancers and cell lines. | |
1745 | <span | |
1746 | class="ptmri7t-x-x-120">BMC Medical Genomics</span>, 4(1):75, 2011 | |
1747 | <!--l. 677--><p class="noindent" >In this work <span | |
1748 | class="ptmri7t-x-x-120">Vmatch </span>was used to align sections of reads against RefSeq | |
1749 | mRNA exon sequences. | |
1750 | ||
1751 | ||
1752 | ||
1753 | </p></li> | |
1754 | <li | |
1755 | class="enumerate" id="x1-14016x8"><a | |
1756 | id="XKID:CHE:WAN:JAC:ZHA:BOY:FIR:TAN:GAE:COL:2012"></a>Marie J Kidd, Zhiliang Chen, Yan Wang, Katherine J Jackson, Lyndon | |
1757 | Zhang, Scott D Boyd, Andrew Z Fire, Mark M Tanaka, Bruno A Gaëta, | |
1758 | and Andrew M Collins. The inference of phased haplotypes for the | |
1759 | immunoglobulin h chain v region gene loci by analysis of vdj gene | |
1760 | rearrangements. <span | |
1761 | class="ptmri7t-x-x-120">The Journal of Immunology</span>, 188(3):1333–1340, 2012 | |
1762 | <!--l. 680--><p class="noindent" >In this work <span | |
1763 | class="ptmri7t-x-x-120">Vmatch </span>was used to align sets of genes. | |
1764 | </p></li> | |
1765 | <li | |
1766 | class="enumerate" id="x1-14018x9"><a | |
1767 | id="XYAM:IKE:BOE:HOR:TAK:URA:KAI:CAR:KAW:HAY:2014"></a>Ryonosuke Yamaga, Kazuhiro Ikeda, Joost Boele, Kuniko Horie-Inoue, | |
1768 | Ken-ichi Takayama, Tomohiko Urano, Kaoru Kaida, Piero Carninci, | |
1769 | Jun Kawai, Yoshihide Hayashizaki, et al. Systemic identification of | |
1770 | estrogen-regulated genes in breast cancer cells through cap analysis | |
1771 | of gene expression mapping. <span | |
1772 | class="ptmri7t-x-x-120">Biochemical and biophysical research</span> | |
1773 | <span | |
1774 | class="ptmri7t-x-x-120">communications</span>, 447(3):531–536, 2014 | |
1775 | <!--l. 683--><p class="noindent" >In this work <span | |
1776 | class="ptmri7t-x-x-120">Vmatch </span>was used to determine the positions of CAGE tags on | |
1777 | the human genome. | |
1778 | </p> | |
1779 | </li></ol> | |
1780 | <!--l. 688--><p class="noindent" > | |
1781 | </p> | |
1782 | <h4 class="likesubsectionHead"><a | |
1783 | id="x1-15000"></a>Current Usages for different Model Organisms</h4> | |
1784 | <!--l. 689--><p class="noindent" > | |
1785 | </p><ol class="enumerate1" > | |
1786 | <li | |
1787 | class="enumerate" id="x1-15002x1"><a | |
1788 | id="XSCZ:BECK:BRI:GIE:ALT:2005"></a>A. Sczyrba, M. Beckstette, A.H. Brivanlou, R. Giegerich, and C.R. | |
1789 | Altmann. Xendb: Full length cDNA prediction and cross species mapping | |
1790 | in <span | |
1791 | class="ptmri7t-x-x-120">xenopus laevis</span>. <span | |
1792 | class="ptmri7t-x-x-120">BMC Genomics</span>, 2005 | |
1793 | <!--l. 706--><p class="noindent" >In this work <span | |
1794 | class="ptmri7t-x-x-120">Vmatch </span>was used to cluster 317 242 EST and cDNA sequences | |
1795 | from <span | |
1796 | class="ptmri7t-x-x-120">Xenopus laevis</span>. <span | |
1797 | class="ptmri7t-x-x-120">Vmatch </span>was chosen for the following reasons: | |
1798 | </p> | |
1799 | ||
1800 | ||
1801 | ||
1802 | <ul class="itemize1"> | |
1803 | <li class="itemize">At first, there was no clustering tool available which could handle large | |
1804 | data sets efficiently, and which was documented well enough to allow | |
1805 | a detailed b replication and evaluation of existing clusters. | |
1806 | </li> | |
1807 | <li class="itemize">Second, <span | |
1808 | class="ptmri7t-x-x-120">Vmatch </span>identifies similarities between sequences rapidly, and | |
1809 | it provides additional options to cluster a set of sequences based on | |
1810 | these matches. Furthermore, the <span | |
1811 | class="ptmri7t-x-x-120">Vmatch </span>output provides information | |
1812 | about how the clusters were derived. Due to the efficiency of <span | |
1813 | class="ptmri7t-x-x-120">Vmatch</span>, it | |
1814 | was possible to perform the clustering for a wide variety of parameters | |
1815 | on the complete sequence set. This allows to study the effect of the | |
1816 | parameter choice on the clustering.</li></ul> | |
1817 | </li> | |
1818 | <li | |
1819 | class="enumerate" id="x1-15004x2"><a | |
1820 | id="XSPIT:LOR:CUL:SCZ:FUEL:2006"></a>M. Spitzer, S. Lorkowski, P. Cullen, A. Sczyrba, and G. Fuellen. Distinguishing | |
1821 | isoforms and paralogs on the protein level. <span | |
1822 | class="ptmri7t-x-x-120">BMC Bioinformatics</span>, 7:110, | |
1823 | 2006 | |
1824 | <!--l. 709--><p class="noindent" >In this work <span | |
1825 | class="ptmri7t-x-x-120">Vmatch </span>was used to cluster EST-sequences of <span | |
1826 | class="ptmri7t-x-x-120">Xenopus</span> | |
1827 | <span | |
1828 | class="ptmri7t-x-x-120">laevis</span>. | |
1829 | </p></li> | |
1830 | <li | |
1831 | class="enumerate" id="x1-15006x3"><a | |
1832 | id="XEIS:COY:WU:WU:THI:WOR:BAD:REN:AME:JON:2006"></a>J.A. Eisen, R.S. Coyne, M. Wu, D. Wu, M. Thiagarajan, J.R. Wortman, J.H. | |
1833 | Badger, Q. Ren, P. Amedeo, and K.M. Jones et al. Macronuclear Genome | |
1834 | Sequence of the Ciliate Tetrahymena thermophila, a Model Eukaryote. <span | |
1835 | class="ptmri7t-x-x-120">PLoS</span> | |
1836 | <span | |
1837 | class="ptmri7t-x-x-120">Biology</span>, 4(9):e286, 2006 | |
1838 | <!--l. 713--><p class="noindent" >In this work <span | |
1839 | class="ptmri7t-x-x-120">Vmatch </span>was used to search exact repeats in the Macronuclear | |
1840 | Genome Sequence of the Ciliate <span | |
1841 | class="ptmri7t-x-x-120">Tetrahymena thermophila</span>. | |
1842 | </p></li> | |
1843 | <li | |
1844 | class="enumerate" id="x1-15008x4"><a | |
1845 | id="XFAU:FOR:CHA:SCHRO:HAY:CAR:HUM:GRI:2008"></a>G. J. Faulkner, A. R. Forrest, A. M. Chalk, K. Schroder, Y. Hayashizaki, | |
1846 | P. Carninci, D. A. Hume, and S. M. Grimmond. A rescue strategy for | |
1847 | multimapping short sequence tags refines surveys of transcriptional activity by | |
1848 | CAGE. <span | |
1849 | class="ptmri7t-x-x-120">Genomics</span>, 91(3):281–288, Mar 2008 | |
1850 | <!--l. 736--><p class="noindent" >In this work <span | |
1851 | class="ptmri7t-x-x-120">Vmatch </span>was used for mapping </p> | |
1852 | <ul class="itemize1"> | |
1853 | <li class="itemize">11 567 973 FANTOM3 mouse CAGE tags to the mouse genome with | |
1854 | minimum match length of 18 bp, a single internal mismatch allowed, | |
1855 | ||
1856 | ||
1857 | ||
1858 | and multiple mismatches allowed at tag ends. | |
1859 | </li> | |
1860 | <li class="itemize">Affymetrix GNF probe sequences to transcripts without allowing for | |
1861 | mismatches.</li></ul> | |
1862 | </li> | |
1863 | <li | |
1864 | class="enumerate" id="x1-15010x5"><a | |
1865 | id="XPRI:JOR:2008"></a>Jittima Piriyapongsa and I King Jordan. Dual coding of sirnas and mirnas by | |
1866 | plant transposable elements. <span | |
1867 | class="ptmri7t-x-x-120">RNA</span>, 14(5):814–821, 2008 | |
1868 | <!--l. 741--><p class="noindent" >In this work <span | |
1869 | class="ptmri7t-x-x-120">Vmatch </span>was used to search small RNA signatures in entire miRNA | |
1870 | gene sequences for Arabidopsis and rice. | |
1871 | </p></li> | |
1872 | <li | |
1873 | class="enumerate" id="x1-15012x6"><a | |
1874 | id="XTAF:GLA:LASS:HAY:CAR:MAT:2009"></a>R. J. Taft, E. A. Glazov, T. Lassmann, Y. Hayashizaki, P. Carninci, and J. S. | |
1875 | Mattick. Small RNAs derived from snoRNAs. <span | |
1876 | class="ptmri7t-x-x-120">RNA</span>, 15(7):1233–1240, Jul | |
1877 | 2009 | |
1878 | <!--l. 745--><p class="noindent" >In this work <span | |
1879 | class="ptmri7t-x-x-120">Vmatch </span>was used to map small RNA data sets onto the | |
1880 | corresponding reference genomes for different model organisms. | |
1881 | </p></li> | |
1882 | <li | |
1883 | class="enumerate" id="x1-15014x7"><a | |
1884 | id="XPLE:PAS:BER:AKA:CAR:VAS:LAZ:SEV:VLA:SIM:2012"></a>C. Plessy, G. Pascarella, N. Bertin, A. Akalin, C. Carrieri, A. Vassalli, | |
1885 | D. Lazarevic, J. Severin, C. Vlachouli, R. Simone, et al. Promoter architecture | |
1886 | of mouse olfactory receptor genes. <span | |
1887 | class="ptmri7t-x-x-120">Genome research</span>, 22(3):486–497, | |
1888 | 2012 | |
1889 | <!--l. 748--><p class="noindent" >In this work <span | |
1890 | class="ptmri7t-x-x-120">Vmatch </span>was used for mapping Illumina reads to the mouse | |
1891 | genome. | |
1892 | </p></li> | |
1893 | <li | |
1894 | class="enumerate" id="x1-15016x8"><a | |
1895 | id="XKEN:SHI:2012"></a>Nathan J Kenny and Sebastian M Shimeld. Additive multiple k-mer | |
1896 | transcriptome of the keelworm <span | |
1897 | class="ptmri7t-x-x-120">Pomatoceros lamarckii </span>(annelida; serpulidae) | |
1898 | reveals annelid trochophore transcription factor cassette. <span | |
1899 | class="ptmri7t-x-x-120">Development genes and</span> | |
1900 | <span | |
1901 | class="ptmri7t-x-x-120">evolution</span>, 222(6):325–339, 2012 | |
1902 | <!--l. 752--><p class="noindent" >In this work <span | |
1903 | class="ptmri7t-x-x-120">Vmatch </span>was used for redundancy removal in the context of | |
1904 | transcriptome assembly of a keelworm species. | |
1905 | </p></li> | |
1906 | <li | |
1907 | class="enumerate" id="x1-15018x9"><a | |
1908 | id="XGOS:OHM:KOG:SON:TUR:ZAJ:ZAL:GRU:SUN:HAN:2014"></a>Cene Gostin, Robin A Ohm, Tina Kogej, Silva Sonjak, Martina Turk, Janja Zajc, | |
1909 | Polona Zalar, Martin Grube, Hui Sun, James Han, et al. Genome sequencing of | |
1910 | four aureobasidium pullulans varieties: biotechnological potential, stress | |
1911 | ||
1912 | ||
1913 | ||
1914 | tolerance, and description of new species. <span | |
1915 | class="ptmri7t-x-x-120">BMC Genomics</span>, 15(1):549, | |
1916 | 2014 | |
1917 | <!--l. 756--><p class="noindent" >In this work <span | |
1918 | class="ptmri7t-x-x-120">Vmatch </span>was used to remove redundant contigs in a genome project | |
1919 | of four <span | |
1920 | class="ptmri7t-x-x-120">Aureobasidium pullulans </span>varieties. | |
1921 | </p></li> | |
1922 | <li | |
1923 | class="enumerate" id="x1-15020x10"><a | |
1924 | id="XMCM:GAR:BAI:KEM:WAR:CEV:ROB:SCHUL:BAL:HOL:2015"></a>M. McMullan, A. Gardiner, K. Bailey, E. Kemen, B. J. Ward, V. Cevik, | |
1925 | A. Robert-Seilaniantz, T. Schultz-Larsen, A. Balmuth, E. Holub, et al. | |
1926 | Evidence for suppression of immunity as a driver for genomic introgressions and | |
1927 | host range expansion in races of albugo candida, a generalist parasite. <span | |
1928 | class="ptmri7t-x-x-120">eLife</span>, | |
1929 | 4:e04550, 2015 | |
1930 | <!--l. 759--><p class="noindent" >In this work <span | |
1931 | class="ptmri7t-x-x-120">Vmatch </span>was used for merging assemblies of Illumina sequenced | |
1932 | cDNA. | |
1933 | </p></li> | |
1934 | <li | |
1935 | class="enumerate" id="x1-15022x11"><a | |
1936 | id="XMOR:DHA:PAV:TRO:WHE:HEL:2015"></a>C Morandin, K Dhaygude, J Paviala, K Trontti, C Wheat, and H Helanterä. | |
1937 | Caste-biases in gene expression are specific to developmental stage in the ant | |
1938 | formica exsecta. <span | |
1939 | class="ptmri7t-x-x-120">Journal of evolutionary biology</span>, 28(9):1705–1718, | |
1940 | 2015 | |
1941 | <!--l. 773--><p class="noindent" >In this work <span | |
1942 | class="ptmri7t-x-x-120">Vmatch </span>was used to combine and scaffold contigs. | |
1943 | </p> | |
1944 | </li></ol> | |
1945 | <!--l. 778--><p class="noindent" >Total number of usages: 108 | |
1946 | </p><!--l. 780--><p class="noindent" > | |
1947 | </p> | |
1948 | <h3 class="likesectionHead"><a | |
1949 | id="x1-16000"></a>Availability</h3> | |
1950 | <!--l. 781--><p class="noindent" ><span | |
1951 | class="ptmri7t-x-x-120">Vmatch </span>is available for <a | |
1952 | href="http://www.vmatch.de/download.html" >download</a> in executable form for the following platforms: | |
1953 | </p> | |
1954 | <ul class="itemize1"> | |
1955 | <li class="itemize">Linux | |
1956 | ||
1957 | ||
1958 | ||
1959 | </li> | |
1960 | <li class="itemize">Mac OS X | |
1961 | </li> | |
1962 | <li class="itemize">MS Windows</li></ul> | |
1963 | <!--l. 794--><p class="noindent" > | |
1964 | </p> | |
1965 | <h3 class="likesectionHead"><a | |
1966 | id="x1-17000"></a>Developer</h3> | |
1967 | <!--l. 795--><p class="noindent" ><span | |
1968 | class="ptmri7t-x-x-120">Vmatch </span>was developed since May 2000 by <a | |
1969 | href="http://www.zbh.uni-hamburg.de/kurtz" >Stefan Kurtz</a>, a professor of Computer | |
1970 | Science at the Center for Bioinformatics, University of Hamburg, Germany. | |
1971 | </p><!--l. 809--> <b>Important Documents</b> <ul> <li> The <a href="virtman.pdf"><i>Vmatch</i>-manual</a> </li> </ul> | |
1972 | <!--l. 817--> <div id="footer"> Copyright © 2000-2017 <a href="mailto:kurtz@zbh.uni-hamburg.de"> Stefan Kurtz</a>. Last update: 2017-06-15 </div> | |
1973 | <!--l. 839--> <!-- Piwik --> <div id="piwik"> <script type="text/javascript"> var pkBaseURL = "https://zenlicensemanager.com/piwik/"; document.write(unescape("</script><script type="text/javascript"> try { var piwikTracker = Piwik.getTracker(pkBaseURL + "piwik.php", 3); piwikTracker.trackPageView(); piwikTracker.enableLinkTracking(); } catch( err ) {} </script> <br/> <noscript> <img src="https://zenlicensemanager.com/piwik/piwik.php?idsite=3" style="border:0" alt=""/> </noscript> <!-- End Piwik Tracking Tag --> </div> | |
1974 | ||
1975 | </body></html> | |
1976 | ||
1977 | ||
1978 | ||
1979 |
0 | #!/usr/bin/env ruby | |
1 | ||
2 | def remove_html_tags(s) | |
3 | re = /<("[^"]*"|'[^']*'|[^'">])*>/ | |
4 | return s.gsub(re, "") | |
5 | end | |
6 | ||
7 | ARGV.each do |filename| | |
8 | file = File.open(filename, "rb") | |
9 | contents = file.read | |
10 | print remove_html_tags(contents) | |
11 | end |
0 | #!/usr/bin/env ruby | |
1 | ||
2 | STDIN.each_line do |line| | |
3 | if line.match(/<meta name=\"src\" content="vmweb.tex"/) | |
4 | print "#{line}" | |
5 | puts <<'HEADER' | |
6 | <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1"/> | |
7 | <meta name="description" CONTENT="The Vmatch large scale sequence analysis | |
8 | software is a versatile software tool for efficiently solving large scale sequence matching tasks."/> | |
9 | <meta name="keywords" CONTENT="sequence analysis, sequence mapping, BLAST, bioinformatics, computational biology"/> | |
10 | <meta http-equiv="Content-Style-Type" content="text/css"/> | |
11 | HEADER | |
12 | elsif line.match(/class=\"titleHead|author|date\"/) | |
13 | print line.gsub(/class=/,"align=\"center\" class=").gsub(/h2/,"h1") | |
14 | elsif line.match(/\/h2/) | |
15 | print line.gsub(/\/h2/,"\/h1") | |
16 | else | |
17 | print line | |
18 | end | |
19 | end |
0 | #!/usr/bin/env ruby | |
1 | ||
2 | puts STDIN.read.gsub!(/<p class=\"noindent\" > <!--delete paragraph-->(.*)\n?<\/p\>/,"\\1\n") |
0 | body { | |
1 | font-family: Verdana, Geneva, Arial, sans-serif; | |
2 | } | |
3 | h1, h2, h3, h4, h5, h6 { | |
4 | color:black; | |
5 | } | |
6 | #w3checklogo { | |
7 | float: right; | |
8 | clear: right; | |
9 | } | |
10 | #downloadbox { | |
11 | float: right; | |
12 | clear: right; | |
13 | width: 280px; | |
14 | padding-right: 20px; | |
15 | } | |
16 | #downloadbox li { | |
17 | list-style-type: none; | |
18 | } | |
19 | #downloadbox li a { | |
20 | list-style-type: none; | |
21 | border : 1px solid black; | |
22 | display: block; | |
23 | padding: 4px 15px 4px 15px; | |
24 | text-decoration: none; | |
25 | } | |
26 | #downloadbox li a:link { | |
27 | color: black; | |
28 | background: rgb(90%, 90%, 20%); | |
29 | } | |
30 | #downloadbox li a:visited { | |
31 | color: gray; | |
32 | background: rgb(90%, 90%, 20%); | |
33 | } | |
34 | #downloadbox li a:hover { | |
35 | color: white; | |
36 | background: rgb(60%, 60%, 90%); | |
37 | } | |
38 | #footer { | |
39 | font-size: 66%; | |
40 | text-align: center; | |
41 | margin-top: 20px; | |
42 | background-color: #DDDDDD; | |
43 | } |
0 | \documentclass[12pt]{article} | |
1 | \usepackage{ifpdf} | |
2 | \usepackage{graphicx} | |
3 | \usepackage{mathptmx} | |
4 | \usepackage{natbib} | |
5 | \usepackage{numprint} | |
6 | \usepackage{bibentry} | |
7 | \usepackage{xspace} | |
8 | \usepackage[latin1]{inputenc} | |
9 | \usepackage{hyperref} | |
10 | \hypersetup{% | |
11 | colorlinks=true, | |
12 | linkcolor=blue | |
13 | } | |
14 | ||
15 | \newcommand{\Vmatch}[0]{\textit{Vmatch}\xspace} | |
16 | \newcommand{\Mybibentry}[2]{\item \bibentry{#1} \par% | |
17 | In this work \Vmatch was used \xspace #2\xspace} | |
18 | %\newcommand{\href}[2]{#2} | |
19 | %\nobibliography* | |
20 | \newcounter{Allusages} | |
21 | \newcommand{\Updateusages}{\addtocounter{Allusages}{\theenumi}} | |
22 | \newcommand{\PrintVol}[1]{#1} | |
23 | \newcommand{\Includegraphics}[2]{% | |
24 | \includegraphics[#1]{#2.pdf} | |
25 | } | |
26 | ||
27 | \makeatletter | |
28 | \edef\texforht{TT\noexpand\fi | |
29 | \@ifpackageloaded{tex4ht} | |
30 | {\noexpand\iftrue} | |
31 | {\noexpand\iffalse}} | |
32 | \makeatother | |
33 | \ifpdf | |
34 | \newcommand{\HCode}[1]{} | |
35 | \fi | |
36 | ||
37 | \title{The \Vmatch large scale sequence analysis software} | |
38 | \author{Stefan Kurtz} | |
39 | \date{\today} | |
40 | \parskip5pt | |
41 | \parindent0pt | |
42 | \begin{document} | |
43 | \maketitle | |
44 | ||
45 | \bibliographystyle{plain} | |
46 | \nobibliography{defines,ltr,assembly,algorithms,rnafolding,commolbio,biotools,kurtz,genomes,strings,genetics,metagenomes} | |
47 | ||
48 | \HCode{ | |
49 | <!--delete paragraph--> | |
50 | <br/> | |
51 | <center> | |
52 | <img src="matchgraph.gif" | |
53 | alt="show matches of different sizes in a matchgraph"/> | |
54 | </center> | |
55 | <div id="downloadbox"> | |
56 | <ul> | |
57 | <li><a href="download.html">Download <i>Vmatch</i>!</a></li> | |
58 | </ul> | |
59 | </div> | |
60 | } | |
61 | ||
62 | This is the web-site for \Vmatch, | |
63 | a versatile software tool for efficiently | |
64 | solving large scale se\-quence matching tasks. | |
65 | \Vmatch subsumes the software tool | |
66 | \href{http://bibiserv.techfak.uni-bielefeld.de/reputer}{REPuter}, | |
67 | but is much more general, with a very flexible user interface, | |
68 | and improved space and time requirements. | |
69 | \HCode{ | |
70 | <a href="vmweb.pdf">Here</a> is a printable version of this | |
71 | HTML-page in PDF. | |
72 | } | |
73 | ||
74 | \section*{Features of \Vmatch} | |
75 | The \href{virtman.pdf}{\Vmatch-manual} | |
76 | gives many examples on how to use \Vmatch. Here are the program's most | |
77 | important features. | |
78 | ||
79 | \input{introduction.inc} | |
80 | ||
81 | \HCode{ | |
82 | <a href="Dataflowfig.pdf">Here</a> is an overview of the dataflow | |
83 | in <i>Vmatch</i>. | |
84 | } | |
85 | ||
86 | \section*{Related tools} | |
87 | There are several tools which are | |
88 | based on the persistent index of \Vmatch: | |
89 | ||
90 | \begin{description} | |
91 | \item[Genalyzer] | |
92 | is a graphical user interface | |
93 | to visualize the output of \Vmatch in form of a match graph. | |
94 | For details see | |
95 | ||
96 | \bibentry{CHO:SCHLE:KUR:GIE:2004} | |
97 | ||
98 | Genalyzer is not available any more. | |
99 | \item[\href{http://bibiserv.techfak.uni-bielefeld.de/mga/}{MGA}] | |
100 | is a program to compute multiple alignments of complete | |
101 | genomes. For details see | |
102 | ||
103 | \bibentry{HOEH:KUR:OHL:2002} | |
104 | \item[Multimat] is a program to compute multiple exact matches between | |
105 | three or more genome size sequences. For details see | |
106 | ||
107 | \bibentry{OHL:KUR:2008} | |
108 | ||
109 | Please contact | |
110 | \href{http://www.zbh.uni-hamburg.de/kurtz}{Stefan Kurtz} if you are interested | |
111 | in using Multimat. | |
112 | ||
113 | \item[\href{http://bibiserv.techfak.uni-bielefeld.de/possumsearch/}{PossumSearch}] | |
114 | Is a program to search for position specific scoring matrices. | |
115 | For details, see | |
116 | ||
117 | \bibentry{BEC:HOM:GIE:KUR:2006} | |
118 | \item | |
119 | \item[\href{http://www.genomethreader.org/}{GenomeThreader}] | |
120 | is a software tool to compute gene structure predictions. The gene structure | |
121 | predictions are calculated using a similarity-based approach where additional | |
122 | cDNA/EST and/or protein sequences are used to predict gene structures via | |
123 | spliced alignments. \textit{GenomeThreader} uses the matching capabilities | |
124 | of \Vmatch to efficiently map the reference sequence to a genomic | |
125 | sequence. For details, see | |
126 | ||
127 | \bibentry{GRE:BRE:SPA:KUR:2005} | |
128 | \item | |
129 | \item[\href{http://www.biopieces.org/}{Biopieces}] | |
130 | is a collection of bioinformatics tools that can be pieced together in a | |
131 | very easy and flexible manner to perform both simple and complex tasks. | |
132 | Some Biopieces depend on \Vmatch. For details see | |
133 | \url{http://www.biopieces.org/}. | |
134 | \end{description} | |
135 | ||
136 | \HCode{ | |
137 | <a name="CurrentUsage"/> | |
138 | } | |
139 | \section*{Previous and Current Usages} | |
140 | ||
141 | We provide an annotated bibliography listing papers which applied \Vmatch | |
142 | and shortly describe the tasks for which \Vmatch was used. We omit our own | |
143 | papers. The references were collected by a | |
144 | \href{https://scholar.google.de/scholar?q=Vmatch+AND+Kurtz+OR+www.vmatch.de}% | |
145 | {search in Google scholar} | |
146 | (which, as of Jan 2, 2016 retrieved 397 results.) | |
147 | ||
148 | \subsection*{Usages in Plant Genome Research} | |
149 | \begin{enumerate} | |
150 | \Mybibentry{BRE:KUR:WAL:2002}{ | |
151 | to a compute a non-redundant set from a large collection of protein sequences | |
152 | from Zea-Maize.} | |
153 | ||
154 | Similar applications are described in | |
155 | ||
156 | \bibentry{DON:ROY:FRE:WAL:BRE:2003}. | |
157 | %\item | |
158 | %For the development of the | |
159 | %\href{http://barleypop.vrac.iastate.edu/BarleyBase/content.php}{Barley1 GeneChip} \Vmatch is used to search | |
160 | %against probes. | |
161 | \item | |
162 | PLEXdb is a database for gene expression resources for plants and plant | |
163 | pathogens, see | |
164 | ||
165 | \bibentry{DAS:VAN:HON:WIS:DIC:2012} | |
166 | ||
167 | PLEXdb provides a \Vmatch-based | |
168 | \href{http://www.plantgdb.org/cgi-bin/prj/PLEXdb/ProbeMatch.pl}{web-service} | |
169 | to match PLEXdb probes. | |
170 | ||
171 | \item | |
172 | The assembly of the Arabidopsis thaliana genome from 2004 | |
173 | (GenBank entries of 2/19/04) contained vector sequence contaminations. | |
174 | For example, region \numprint{3617880} to \numprint{3625027} of | |
175 | chromosome II contained | |
176 | a cloning vector. \Vmatch was used to detect the vector contamination, | |
177 | see \href{http://www.plantgdb.org/AtGDB/Annotation/vector.php}{here} | |
178 | ||
179 | \item | |
180 | \bibentry{DON:LAW:SCHLUE:WIL:KUR:LUS:BRE:2005} | |
181 | ||
182 | This work describes PlantGDB, which | |
183 | provides a service called | |
184 | \href{http://www.plantgdb.org/PlantGDB-cgi/vmatch/patternsearch.pl}{PatternSearch@PlantGDB} | |
185 | for genome wide pattern searches in plant sequences. The service is based | |
186 | on \Vmatch. | |
187 | \Mybibentry{LIN:KRO:2005}{ | |
188 | for three different tasks: | |
189 | \begin{itemize} | |
190 | \item | |
191 | Searching spliced mRNA in the Arabidopsis genome to detect | |
192 | micromatches of length at least 20 with maximum 2 mismatches. | |
193 | \item | |
194 | Finding matches of length at least 15 long with at most one mismatch | |
195 | between predicted mature miRNA-sequences and a set of ESTs as well | |
196 | as sequences from the Arabidopsis Small RNA Project (ASRP). | |
197 | \item | |
198 | Aligning and performing single linkage clustering | |
199 | of the predicted mature miRNA sequences. Candidate pairs aligning over at least | |
200 | 17 bases, allowing an edit distance of 1 were grouped in the same family. | |
201 | \end{itemize}} | |
202 | ||
203 | \item | |
204 | \bibentry{POM:LEM:TUR:2006} | |
205 | ||
206 | \bibentry{TUR:OTI:LEM:2006} | |
207 | ||
208 | In these papers \Vmatch was used to search | |
209 | and compare repeated elements in different chloroplast DNA. | |
210 | ||
211 | \item | |
212 | \bibentry{SPA:NOU:HAA:YAN:GUN:HIN:KLE:HAB:SCHOO:MAY:2007} | |
213 | In this work about the \textit{MIPSPlantsDB} database | |
214 | \Vmatch was used to cluster large sequence sets. | |
215 | ||
216 | \Mybibentry{SCHIJ:VOS:MAR:JON:ROS:MOL:TIK:ANG:TUN:BOV:2007}{ | |
217 | to compare target genes of the tomato Chs RNAi to a tomato gene index.} | |
218 | ||
219 | \Mybibentry{LIN:JAC:NYG:MAN:KRO:2007}{ | |
220 | to search different | |
221 | plant genomes for matches of length at least 20 with maximum of 2 mismatches. | |
222 | Here the fact that \Vmatch is an exhaustive search tool is important.} | |
223 | ||
224 | \Mybibentry{DEC:OTI:THU:LEM:2007}{ | |
225 | to determine the presence of shared repeated elements of minimum length | |
226 | 30, with up to 10\% mismatches using in different sequence sets from | |
227 | the green alga \textit{Leptosira terrestris}.} | |
228 | ||
229 | \Mybibentry{OSS:SCHNE:CLA:LAN:WAR:WEI:2008}{ | |
230 | to map millions of short sequence reads to the \textit{A.~Thaliana} genome. | |
231 | Up to four mismatches and up to three indels were allowed in the matching | |
232 | process. The seed size was chosen to be 0. The reads were aligned using the | |
233 | best match strategy by iteratively increasing the the allowed number of | |
234 | mismatches and gaps at each round.} | |
235 | ||
236 | \Mybibentry{DIBO:OSS:SCHNE:RAT:2008}{ | |
237 | to map millions of short sequence reads to the \textit{A.~Thaliana} genome. | |
238 | \Vmatch was part of a multi-step pipeline, combining a fast | |
239 | matching algorithm (\Vmatch) for initial read mapping and | |
240 | an optimal alignment algorithm based on dynamic programming (QPALMA) | |
241 | for high quality detection of splice sites.} | |
242 | ||
243 | \Mybibentry{ASS:HER:LIN:HUE:TAL:SMA:IMM:ELD:FIE:SCHAT:2010}{ | |
244 | for motif searching in different plant genomes.} | |
245 | ||
246 | \Mybibentry{EVE:SAT:GOL:MEY:BET:SAK:WAR:JAC:2010}{ | |
247 | to map unique consensus sequence tags to the maize reference genome.} | |
248 | ||
249 | \Mybibentry{BRO:OTI:LEM:TUR:2010}{ | |
250 | to identify and cluster repeated sequences in \textit{Floydiella} chloroplast | |
251 | genome.} | |
252 | ||
253 | \Mybibentry{REH:AQU:GRU:HEN:HIL:LAU:NAO:PAT:ROM:SHU:2010}{ | |
254 | to calculate direct and reverse complementary matches of length {17} bp or | |
255 | greater with edit distance {1} or less between five nuclear chromosomes | |
256 | and mitochondrial and chloroplast genome sequences.} | |
257 | ||
258 | \Mybibentry{SEK:LIN:CHI:HAN:BUE:LEO:KAE:2011}{ | |
259 | to search probe sequences against the maize genome | |
260 | the cDNA sequences of the official maize gene models.} | |
261 | ||
262 | \Mybibentry{DAS:OH:HAA:HER:HON:ALI:YUN:BRE:ZHU:BOH:2011}{ | |
263 | for clustering sequences assembled from 454-reads of | |
264 | \textit{Thellungiella parvula}, a model for the evolution of plant | |
265 | adaptation to extreme environments.} | |
266 | ||
267 | \Mybibentry{WIL:HOF:KLE:WEI:2011}{ | |
268 | for grouping short reads into | |
269 | pools representing the same RAD tag.} | |
270 | ||
271 | \Mybibentry{GAO:ZHO:WAN:SU:WAN:2011}{ | |
272 | for detecting and | |
273 | clustering repetitive sequences in diverse fern plastid genomes.} | |
274 | ||
275 | \Mybibentry{SLO:ALV:CHU:WU:MCC:PAL:TAY:2012}{ | |
276 | to precisely | |
277 | define the boundaries of all repeats with 100\% sequence identity.} | |
278 | ||
279 | \Mybibentry{DUB:FAR:SCHLU:CAN:ABE:TUT:WOO:SHA:MUL:KUD:2011}{ | |
280 | cluster sequences based on their six-frame translation.} | |
281 | ||
282 | \Mybibentry{SAX:PEN:UPA:KUM:CAR:SCHLU:FAR:WHA:SAR:MAY:2012}{ | |
283 | to identify reciprocal best matches between the pigeonpea sequences and | |
284 | other legume sequences.} | |
285 | ||
286 | \Mybibentry{HAZ:REE:RIS:PEC:2012}{ | |
287 | for assembly clustering and | |
288 | optimization of contigs for | |
289 | \textit{Neochloris oleoabundans} (a Chlorophyceae class green microalgae).} | |
290 | ||
291 | \Mybibentry{MAR:KLE:BAN:BLA:MAC:SCHMU:SCHOL:GUN:WIC:SIM:2012}{ | |
292 | to match reads against a repeat library to | |
293 | identity the content of the repetitive DNA per sequence read.} | |
294 | ||
295 | \Mybibentry{CHI:DAV:BUE:2011}{ | |
296 | to align individual probes to representative gene models.} | |
297 | ||
298 | \Mybibentry{SEV:DIJ:HAM:2011}{ | |
299 | for performing exact searches with | |
300 | peptides against the filtered proteome of \textit{A. thaliana}.} | |
301 | ||
302 | \Mybibentry{WOL:WEI:SEG:ROS:BEI:DON:SPI:NOR:REH:KOE:2011}{ | |
303 | to map RNAseq reads, | |
304 | allowing up to two mismatches (option \texttt{-h 2}) | |
305 | and generating maximal substring matches | |
306 | that are unique in some reference dataset (option \texttt{-mum cand}).} | |
307 | ||
308 | \Mybibentry{FLE:KHA:JOH:YOU:MIT:WRE:HES:FOS:SCHAR:SCO:2011}{ | |
309 | to identify terminal inverted repeats of length range {10-65} bp, | |
310 | $\geq 80\%$ identity, maximum inter-TIR distance 650~bp in in genomes of | |
311 | epichloid fungal endophytes of grasses.} | |
312 | ||
313 | \Mybibentry{CHI:KON:BUE:2012}{ | |
314 | to match putative unique transcript sequence assemblies.} | |
315 | ||
316 | \Mybibentry{CHE:CAS:BAI:RED:MIC:2012}{ | |
317 | for refining assemblies of Illumina reads in the context of a transcriptome | |
318 | project for plant virus vector \textit{Graminella nigrifrons}.} | |
319 | ||
320 | \Mybibentry{KRI:PAT:JAI:GAU:CHOU:VAI:DEE:HAR:KRI:NAI:2012}{ | |
321 | for clustering repeats and for building a consensus repeat library in the | |
322 | context of genome and transcriptome projects for \textit{Azadirachta indica}, a | |
323 | medicinal and pesticidal angiosperm.} | |
324 | ||
325 | \Mybibentry{LIU:KUM:ZHA:ZHE:WAR:2012}{ | |
326 | to map unique consensus sequences tags to the maize reference | |
327 | genome and to predict targets of novel miRNAs.} | |
328 | ||
329 | \Mybibentry{BOU:KOU:PAV:MIN:TSA:DAR:2012}{ | |
330 | for masking Long Terminal Repeats in the Maize Genome Sequence.} | |
331 | ||
332 | \item In the papers | |
333 | ||
334 | \bibentry{HER:MAR:DOR:PFE:GAL:SCHAA:JOU:SIM:VAL:DOL:2012} | |
335 | ||
336 | \bibentry{PHI:PAU:BER:SOU:CHO:LAU:SIM:SAF:BEL:VAU:2013} | |
337 | ||
338 | \Vmatch was used to mask repetitive DNA. | |
339 | ||
340 | \Mybibentry{HOW:YU:KNA:CRO:KOL:DOL:LOR:DEA:2013}{ | |
341 | to cluster \numprint{40010} assembled isotigs.} | |
342 | ||
343 | \Mybibentry{KAR:HAA:MAL:GEE:BOV:LAM:ANG:MAA:2013}{ | |
344 | to preprocess short reads in the context of identifying mircoRNA targets in | |
345 | tomato fruit development.} | |
346 | ||
347 | \Mybibentry{GRO:MAR:SIM:ABR:WAN:VIS:2013}{ | |
348 | in an all-vs-all comparison to bin contigs into | |
349 | loci based on a minimum of 200~bp sequence overlap in the context of | |
350 | transcriptome assembly for two Agave-species.} | |
351 | ||
352 | \Mybibentry{KAN:HEL:DUR:WIN:ENG:BEH:HOL:BRA:HAU:FER:2013}{ | |
353 | to align 454-reads to assembled isotigs for Ragweed pollen.} | |
354 | ||
355 | \Mybibentry{KUG:SIE:NUS:AME:SPAN:STEI:LEM:MAY:BUE:SCHWE:2013}{ | |
356 | for comparing gene sets.} | |
357 | ||
358 | \Mybibentry{MAR:ZHO:HAS:SCHMU:VRA:KUB:KOEN:KUG:SCHOL:HAC:2013}{ | |
359 | to detect repetitive DNA content of chromosomal survey | |
360 | sequences from the Rye genome.} | |
361 | ||
362 | \item | |
363 | In the papers | |
364 | ||
365 | \bibentry{KOP:MAR:VHA:HRV:VRA:BAR:KOP:CAT:STO:NOV:2013} | |
366 | ||
367 | \bibentry{KOP:MAR:CHA:HRI:VRA:BAR:2013} | |
368 | ||
369 | \Vmatch was used for | |
370 | identifying repetitive DNA content in contigs of meadow fescue chromosome 4F | |
371 | assembled from Illumina short reads. | |
372 | ||
373 | \item | |
374 | In the papers | |
375 | ||
376 | \bibentry{JAY:WAN:YU:TAC:PEL:COL:REN:VOI:2011} | |
377 | ||
378 | \bibentry{WAN:WEI:SMI:2013} | |
379 | ||
380 | \Vmatch was used for mapping siRNA sequences to the | |
381 | \textit{Arabidopsis thaliana} genome. | |
382 | ||
383 | \Mybibentry{HEN:VIV:DES:CHAU:PAY:GUT:CAS:2014}{ | |
384 | for the identification of binding motifs.} | |
385 | ||
386 | \Mybibentry{WAN:HAB:GUN:GLAE:NUS:LUO:LOM:BOR:KER:SHA:2014}{ | |
387 | for masking one sequence set with another and for | |
388 | mapping miRNA sequences of all plant species present in a reference database | |
389 | to whole-genome assembly of \textit{Spirodela polyrhiza}.} | |
390 | ||
391 | \Mybibentry{LOG:SCHEL:NUR:SAM:PEN:2014}{ | |
392 | for repeat detection.} | |
393 | ||
394 | \Mybibentry{WAN:SHI:RIN:2015}{ | |
395 | to eliminate redundancies in assemblies of Illumina reads in | |
396 | the context of studying plant defense mechanisms.} | |
397 | ||
398 | \Mybibentry{ASH:HUL:WAN:YAN:GUA:JON:MAT:MOC:CHE:STE:2015}{ | |
399 | for clustering to determine a non-redundant set of assembled contigs.} | |
400 | ||
401 | \Mybibentry{UST:NOV:BLI:SMY:2015}{ | |
402 | for clustering sequences based on their RT and aRNH domain.} | |
403 | ||
404 | \Mybibentry{HLE:RIV:CLA:MAR:VAN:GON:GAR:LER:SIM:VAL:2015}{ | |
405 | for identifying repeats in contigs assembled from 454-reads.} | |
406 | ||
407 | \Mybibentry{SHE:YAN:LU:WAN:SON:2015}{ | |
408 | for identifying inverted repeats in chloroplast genomes.} | |
409 | ||
410 | \Mybibentry{PAN:MOH:KHA:MEH:EBR:2015}{ | |
411 | to identify contaminations and repetitive elements by | |
412 | comparison of mRNA sequences to vector, bacterial and repeat databases.} | |
413 | ||
414 | \Mybibentry{WOL:TWO:GAD:KNA:GRU:GEN:2015}{ | |
415 | to cluster contigs of different assemblies into groups of homologous sequences.} | |
416 | ||
417 | \Mybibentry{YAN:LU:SHE:YAN:XU:SON:2015}{ | |
418 | to identify inverted repeats in chloroplast genomes.} | |
419 | ||
420 | \Updateusages | |
421 | \end{enumerate} | |
422 | ||
423 | \subsection*{Usages in the Microbial Genome Research} | |
424 | \begin{enumerate} | |
425 | \item | |
426 | The | |
427 | \href{http://www.llnl.gov/str/April04/Slezak.html}{KPATH system}, | |
428 | developed at the Lawrence Livermore National Laboratories, and | |
429 | described in | |
430 | ||
431 | \bibentry{FIT:GAR:KUC:KUR:MYE:OTT:SLE:VIT:ZEM:MCC:2002} | |
432 | ||
433 | \bibentry{SLE:KUC:OTT:TOR:MED:SMI:TRU:MUL:LAM:VIT:ZEM:ZHO:GAR:2003} | |
434 | ||
435 | used \Vmatch to detect unique substrings in large | |
436 | collection of DNA sequences. These unique substrings serve as | |
437 | signatures allowing for rapid and accurate diagnostics | |
438 | to identify pathogen bacteria and viruses. A similar application | |
439 | is reported in \bibentry{GAR:KUC:VIT:SLE:2003}. | |
440 | ||
441 | \Mybibentry{POB:WET:SZY:SCHIL:KUR:MEY:NAT:BECK:2006}{ | |
442 | to map signature tags to the genome | |
443 | of \textit{S.~meliloti}.} | |
444 | ||
445 | \item | |
446 | The | |
447 | \href{http://crispr.u-psud.fr/Server/CRISPRfinder.php}{CRISPRFinder}-program | |
448 | and the | |
449 | \href{http://crispr.u-psud.fr/crispr/CRISPRdatabase.php}{CRISPRdatabase}, described in | |
450 | ||
451 | \bibentry{GRI:VER:POU:2007A} | |
452 | ||
453 | \bibentry{GRI:VER:POU:2007B} | |
454 | ||
455 | used \Vmatch to | |
456 | efficiently find maximal repeats, as a first step in localizing | |
457 | Clustered regularly interspaced short palindromic repeats (CRISPRs). | |
458 | ||
459 | \Mybibentry{VOSS:GEO:SCHOE:UDE:HES:2009}{ | |
460 | to map predicted sequences to | |
461 | information about Rho-independent terminators provided by a specific database.} | |
462 | ||
463 | \Mybibentry{SCHMU:CAN:SCHLU:MA:MIT:NEL:HYT:SON:THE:CHE:2010}{ | |
464 | to cluster DNA-sequences into families based on their | |
465 | six-frame translation.} | |
466 | ||
467 | \Mybibentry{ZIM:GES:CHE:LOR:SCHRO:2010}{ | |
468 | to align 454-sequences to the Ecoli-genome and to cluster the sequences.} | |
469 | ||
470 | \Mybibentry{TOU:DEN:MED:BAR:ELK:PET:2010}{ | |
471 | for detecting repeats in three bacterial species.} | |
472 | ||
473 | \Mybibentry{MAY:MAR:HED:SIM:LIU:MOR:STEU:TAU:ROE:GUN:2011}{ | |
474 | for masking repeats in 454-reads.} | |
475 | ||
476 | \Mybibentry{PUS:MAN:JI:LI:EVA:CRA:MOR:MEA:SIN:SAX:2011}{ | |
477 | to identify distal primers.} | |
478 | ||
479 | \Mybibentry{BRE:SHE:POP:2011}{ | |
480 | for removing redundant transcripts assembled in an RNA-seq study based on | |
481 | Illumina reads for \textit{Heliothis virescens} (tobacco budworm), infected | |
482 | with a virus.} | |
483 | ||
484 | \Mybibentry{TRI:HAM:BUE:TIS:VER:ZIN:LEA:2011}{ | |
485 | to search unassembled Illumina reads of US and African strains of | |
486 | \textit{Xanthomonas oryzae} for evidence of transcriptional activator-like | |
487 | effector sequences.} | |
488 | ||
489 | \item | |
490 | \Vmatch is used as an integral part of the PriMUX software package described in | |
491 | ||
492 | \bibentry{HYS:NAR:ELS:CAR:WIL:GAR:2012} | |
493 | ||
494 | In this context \Vmatch used for selecting multiplex compatible, | |
495 | degenerate primers and probes to detect diverse targets such as viruses. | |
496 | ||
497 | \Mybibentry{SHE:POP:2012}{ | |
498 | to identify redundant contigs from de novo exome assemblies.} | |
499 | ||
500 | \Mybibentry{HUR:SUL:2013}{ | |
501 | to identify reads which have no common 20-mers with other | |
502 | reads in a context of a marine viral metagenome project.} | |
503 | ||
504 | \Mybibentry{ZHU:RHO:FESCH:2013}{ | |
505 | for clustering potential complete | |
506 | Endogenous retroviruses of the bat \textit{Myotis lucifugus} into subfamilies.} | |
507 | ||
508 | \item In the three papers | |
509 | ||
510 | \bibentry{HUR:WES:BRU:SUL:2014} | |
511 | ||
512 | \bibentry{HUR:DEN:POU:SUL:2013} | |
513 | ||
514 | \bibentry{BRU:HUR:SCHOF:DUC:SUL:2015} | |
515 | ||
516 | \Vmatch was used for $k$-mer analysis in the context of different marine | |
517 | metagenome projects. | |
518 | ||
519 | \Mybibentry{DEC:PAR:2014}{ | |
520 | for $k$-mer analysis in the context of microbial communities.} | |
521 | ||
522 | \Mybibentry{BEN:BOU:FIC:KRI:LAR:2014}{ | |
523 | in an iterative scheme to construct contigs from reads associated with | |
524 | resistance genes in the context of a shotgun metagenome project.} | |
525 | ||
526 | \Mybibentry{NIC:THI:GAR:MCL:FOF:KOS:ELL:BRE:JAC:JAI:2013}{ | |
527 | to match probe candidate sequences against viral sequences and the human | |
528 | genmome sequence.} | |
529 | ||
530 | \Mybibentry{HEN:RUM:SCZ:VEL:DIE:GER:GOM:RAH:STO:BOR:2014}{ | |
531 | to identify the species of the Streptococcaceae | |
532 | by comparing with Silva 115 release 16S reference sequence database.} | |
533 | \Updateusages | |
534 | \end{enumerate} | |
535 | ||
536 | \subsection*{Usages in General Web-Servers or Sequence Analysis Software} | |
537 | \begin{enumerate} | |
538 | \item | |
539 | Since 2000, | |
540 | the \href{http://rsat.ulb.ac.be/rsat/}{RSA-tools}, described in | |
541 | ||
542 | \bibentry{HEL:RIO:COL:2000} | |
543 | ||
544 | and developed by Jacques van Helden | |
545 | use \Vmatch to \href{http://rsat.ulb.ac.be/rsat/purge-sequence_form.cgi}{purge} | |
546 | sequences before computing sequence statistics. Similar applications are | |
547 | reported in the following papers: | |
548 | ||
549 | \bibentry{HUL:WEE:CRO:GER:HEP:HEL:2003} | |
550 | ||
551 | \bibentry{SIM:WOD:COH:HEL:2004} | |
552 | ||
553 | \bibentry{SIM:HEL:COH:WOD:2004}. | |
554 | ||
555 | \item | |
556 | The program \href{http://splicenest.molgen.mpg.de/}{SpliceNest}, described in | |
557 | ||
558 | \bibentry{COW:HAA:VIN:2002} | |
559 | ||
560 | computes gene indices and uses \Vmatch to | |
561 | \href{http://splicenest.molgen.mpg.de/doc/help.html\#mapping}{map} clustered | |
562 | sequences to large genomes. | |
563 | %\item | |
564 | %The oligo design program | |
565 | %\href{http://oligos.molgen.mpg.de/}{Promide} | |
566 | %\bibentry{RAH:2002} developed by | |
567 | %Sven Rahmann is based on the persistent index structure of \Vmatch. | |
568 | %Promide uses \textit{mkvtree} for generating the index. | |
569 | \item | |
570 | \href{http://bibiserv.techfak.uni-bielefeld.de/e2g/}{e2g} | |
571 | is a web-based server which efficiently maps large | |
572 | EST and cDNA data sets to genomic DNA. The use of \Vmatch | |
573 | allows to significantly extend the size of data that can be mapped in | |
574 | reasonable time. e2g is available as a web service and hosts | |
575 | large collections of EST sequences (e.g.\ 4.1 million mouse ESTs | |
576 | of 1.87 Gbp) in a precomputed persistent index. For details see | |
577 | ||
578 | \bibentry{KRUE:SCZ:KUR:GIE:2004}. | |
579 | ||
580 | \item | |
581 | The \href{http://bibiserv.techfak.uni-bielefeld.de/}{Bielefeld Bioinformatics Server} provides the | |
582 | \href{http://bibiserv.techfak.uni-bielefeld.de/reputer/}{REPuter} | |
583 | web-service to compute repeats in complete genomes. The service is based on | |
584 | \Vmatch. | |
585 | ||
586 | \Mybibentry{FER:DON:SCHNE:MOR:NAN:BRE:WAL:2004}{ | |
587 | to (1) match \numprint{130861} vector-trimmed sequences against the maize | |
588 | repeat database, and (2) to cluster near-identical sequences. } | |
589 | %The \href{http://www.mutransposon.org/project/RescueMu/research/GSSanalysis}% | |
590 | %{Mu Transposon Information Resource}, | |
591 | \item | |
592 | \href{http://www-ab.informatik.uni-tuebingen.de/software/crosslink/welcome.html}{CrossLink}, described in | |
593 | ||
594 | \bibentry{DEZ:SCHAEF:WIE:WEI:HUS:2006} | |
595 | ||
596 | is a versatile computational tool which aids in visualizing | |
597 | relationships between RNA sequences (particularly between ncRNAs and | |
598 | their putative target transcripts) in an intuitive and accessible way. | |
599 | Besides BLAST, CrossLink uses \Vmatch to reveal the sequence | |
600 | relationships to be visualized. | |
601 | ||
602 | \item | |
603 | The early version of the web-service \href{http://mips.gsf.de/simap/}% | |
604 | {Similarity matrix of Proteins (SIMAP)}, see | |
605 | ||
606 | \bibentry{ARN:RAT:TIS:TRU:STU:MEW:2005} | |
607 | ||
608 | used \Vmatch to locate | |
609 | the sequences in SIMAP which are similar to a given query. This is much | |
610 | faster than running BLAST. | |
611 | ||
612 | \Mybibentry{FIE:VAN:PEE:VAN:NAP:2005}{ | |
613 | to compute similarities between genomes, which are then visualized by the | |
614 | program \href{http://www.win.tue.nl/dnavis/}{DNAVis}.} | |
615 | ||
616 | \item In the paper | |
617 | ||
618 | \bibentry{SEI:KRUE:HAR:SCHWA:LOEW:MER:DAN:GIE:2006} | |
619 | ||
620 | Seidel et.\ al.\ describe | |
621 | methods for creating web-services and give examples which, among other tools, | |
622 | also integrate \Vmatch. | |
623 | ||
624 | \item | |
625 | The program \textit{Gepard} | |
626 | ||
627 | \bibentry{KRU:ARN:RAT:2007} | |
628 | ||
629 | uses \textit{mkvtree} to compute enhanced suffix arrays. | |
630 | ||
631 | \item | |
632 | \Vmatch is used a part of the transcriptome assembler software Rnnotator, | |
633 | described in | |
634 | ||
635 | \bibentry{MAR:BRU:FAN:MEN:BLO:ZHA:SHE:SNY:WAN:2010} | |
636 | \item | |
637 | The BioExtract-Server described in | |
638 | ||
639 | \bibentry{LUS:JEN:BRE:2011} | |
640 | ||
641 | uses \Vmatch to remove duplicated sequences. | |
642 | ||
643 | \Mybibentry{LUS:GNI:DOO:2015}{ | |
644 | for removing duplicates in BlastP results. This use is | |
645 | part of a workflow in | |
646 | \href{http://www.myexperiment.org/workflows/3131.html}{myexperiment}. | |
647 | } | |
648 | ||
649 | \Mybibentry{GRE:LOY:HOR:RAT:2015}{ | |
650 | for probe/primer search functionality in the probeBase database.} | |
651 | \Updateusages | |
652 | \end{enumerate} | |
653 | ||
654 | \subsection*{Current Usages in Human Genome Research} | |
655 | \begin{enumerate} | |
656 | \Mybibentry{BUC:JAR:MEN:MAT:SCO:GRE:LAN:DUM:2005}{ | |
657 | to reveal long repeats inside human chromosome 1 and long similar regions | |
658 | between human chromosome 1 and all other human chromosomes.} | |
659 | ||
660 | \Mybibentry{LIA:WAN:LIU:JI:LIU:CHE:WEB:REE:DEA:2007}{ | |
661 | for Vector screening.} | |
662 | ||
663 | \Mybibentry{NYG:JAC:LIN:ERI:BAL:FLY:TOL:MOE:SOE:KRO:LIT:2009}{ | |
664 | for mapping short reads.} | |
665 | ||
666 | \Mybibentry{COL:SOB:LU:THA:BOW:BRO:GRE:BAR:HUT:2009}{ | |
667 | for matching reads to sets of RNA sequences and the Human genome.} | |
668 | ||
669 | \Mybibentry{CLO:WAN:XU:GU:LEA:HEA:BAR:STE:MAR:NOU:2011}{ | |
670 | to uniquely map miRNAs against the human genome.} | |
671 | ||
672 | \Mybibentry{TAK:TSU:KAT:OKA:HOR:IKE:URA:KAW:HAS:IKE:2011}{ | |
673 | to determine the positions of CAGE tags on the human genome.} | |
674 | ||
675 | \Mybibentry{KEV:LAL:LI:CAV:NAR:KAM:MIT:HAK:KOZ:GEN:2011}{ | |
676 | to align sections of reads against RefSeq mRNA exon sequences.} | |
677 | ||
678 | \Mybibentry{KID:CHE:WAN:JAC:ZHA:BOY:FIR:TAN:GAE:COL:2012}{ | |
679 | to align sets of genes.} | |
680 | ||
681 | \Mybibentry{YAM:IKE:BOE:HOR:TAK:URA:KAI:CAR:KAW:HAY:2014}{ | |
682 | to determine the positions of CAGE tags on the human genome.} | |
683 | ||
684 | \Updateusages | |
685 | \end{enumerate} | |
686 | ||
687 | \subsection*{Current Usages for different Model Organisms} | |
688 | \begin{enumerate} | |
689 | \Mybibentry{SCZ:BECK:BRI:GIE:ALT:2005}{ | |
690 | to cluster \numprint{317242} EST and cDNA sequences from | |
691 | \textit{Xenopus laevis}. \Vmatch was chosen for the following reasons: | |
692 | \begin{itemize} | |
693 | \item | |
694 | At first, there was no clustering tool available which could handle | |
695 | large data sets efficiently, and which was documented well enough to | |
696 | allow a detailed b replication and evaluation of existing clusters. | |
697 | \item | |
698 | Second, \Vmatch identifies similarities between sequences rapidly, | |
699 | and it provides additional options to cluster a set of sequences | |
700 | based on these matches. Furthermore, the \Vmatch output provides | |
701 | information about how the clusters were derived. Due to the | |
702 | efficiency of \Vmatch, it was possible to perform the clustering for a | |
703 | wide variety of parameters on the complete sequence set. | |
704 | This allows to study the effect of the parameter choice on the clustering. | |
705 | \end{itemize}} | |
706 | ||
707 | \Mybibentry{SPIT:LOR:CUL:SCZ:FUEL:2006}{ | |
708 | to cluster EST-sequences of \textit{Xenopus laevis}.} | |
709 | ||
710 | \Mybibentry{EIS:COY:WU:WU:THI:WOR:BAD:REN:AME:JON:2006}{ | |
711 | to search exact repeats in the Macronuclear Genome Sequence of the Ciliate | |
712 | \textit{Tetrahymena thermophila}.} | |
713 | %\item | |
714 | %\href{http://www.plantgdb.org/}{PlantGDB} provides a Web Service | |
715 | %named \href{https://biomoby.tigr.org/wiki/index.php/Code_Examples_-_Java}{VMatchForArabidopsis}% | |
716 | % | |
717 | %based on \Vmatch. It allows to search sequences | |
718 | %from \textit{Arabidopsis Thaliana}. | |
719 | %\item | |
720 | %The \href{http://www.jgi.doe.gov/science/posters/LBNL-59860goltsman.pdf}{DOE Joint Genome Institute}% | |
721 | % | |
722 | %used \Vmatch to | |
723 | %identify and mask all continuous non-unique sequence fragments over | |
724 | %500~bp in \textit{Frankia sp.} and \textit{Shewanella oneidensis}. | |
725 | ||
726 | \Mybibentry{FAU:FOR:CHA:SCHRO:HAY:CAR:HUM:GRI:2008}{ | |
727 | for mapping | |
728 | \begin{itemize} | |
729 | \item | |
730 | \numprint{11567973} FANTOM3 mouse CAGE tags to the mouse genome | |
731 | with minimum match length of {18} bp, a single internal mismatch allowed, | |
732 | and multiple mismatches allowed at tag ends. | |
733 | \item | |
734 | Affymetrix GNF probe sequences to transcripts without allowing for mismatches. | |
735 | \end{itemize}} | |
736 | ||
737 | ||
738 | \Mybibentry{PRI:JOR:2008}{ | |
739 | to search small RNA signatures in entire miRNA gene sequences for | |
740 | Arabidopsis and rice.} | |
741 | ||
742 | \Mybibentry{TAF:GLA:LASS:HAY:CAR:MAT:2009}{ | |
743 | to map small RNA data sets onto the corresponding reference | |
744 | genomes for different model organisms.} | |
745 | ||
746 | \Mybibentry{PLE:PAS:BER:AKA:CAR:VAS:LAZ:SEV:VLA:SIM:2012}{ | |
747 | for mapping Illumina reads to the mouse genome.} | |
748 | ||
749 | \Mybibentry{KEN:SHI:2012}{ | |
750 | for redundancy removal in the context of transcriptome assembly of | |
751 | a keelworm species.} | |
752 | ||
753 | \Mybibentry{GOS:OHM:KOG:SON:TUR:ZAJ:ZAL:GRU:SUN:HAN:2014}{ | |
754 | to remove redundant contigs in a genome project of four | |
755 | \textit{Aureobasidium pullulans} varieties.} | |
756 | ||
757 | \Mybibentry{MCM:GAR:BAI:KEM:WAR:CEV:ROB:SCHUL:BAL:HOL:2015}{ | |
758 | for merging assemblies of Illumina sequenced cDNA.} | |
759 | ||
760 | % add applications at Bioinformatics Center Copenhagen Univ., see E-mails from | |
761 | % Feb 2007, this may be the Biopieces. | |
762 | ||
763 | % the following paper cites \Vmatch, but does not use it. | |
764 | % http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1868776 | |
765 | % \bibentry{TEM:ZAV:BOD:CHA:GEY:WAS:BEN:REI:2007}, Tembe et et.\ al.\ | |
766 | ||
767 | %Add "Highly Specific Gene Silencing by Artificial MicroRNAs in Arabidopsis" | |
768 | %of Schwab et al, 2006, and implemented on wmd2.weigelworld.org. | |
769 | %refers to Hypa and not really to \Vmatch. | |
770 | ||
771 | \Mybibentry{MOR:DHA:PAV:TRO:WHE:HEL:2015}{ | |
772 | to combine and scaffold contigs.} | |
773 | ||
774 | \Updateusages | |
775 | \end{enumerate} | |
776 | ||
777 | Total number of usages: \arabic{Allusages} | |
778 | ||
779 | \section*{Availability} | |
780 | \Vmatch is available for | |
781 | \href{http://www.vmatch.de/download.html}{download} | |
782 | in executable form for the following platforms: | |
783 | ||
784 | \begin{itemize} | |
785 | \item | |
786 | Linux | |
787 | \item | |
788 | Mac OS X | |
789 | \item | |
790 | MS Windows | |
791 | \end{itemize} | |
792 | ||
793 | \section*{Developer} | |
794 | \Vmatch was developed since May 2000 by | |
795 | \href{http://www.zbh.uni-hamburg.de/kurtz}{Stefan Kurtz}, | |
796 | a professor of | |
797 | Computer Science at the Center for Bioinformatics, University of Hamburg, | |
798 | Germany. | |
799 | ||
800 | \HCode{ | |
801 | <!--delete paragraph--> | |
802 | <b>Important Documents</b> | |
803 | <ul> | |
804 | <li> | |
805 | The <a href="virtman.pdf"><i>Vmatch</i>-manual</a> | |
806 | </li> | |
807 | </ul> | |
808 | } | |
809 | ||
810 | \HCode{ | |
811 | <!--delete paragraph--> | |
812 | <div id="footer"> | |
813 | Copyright © 2000-2017 <a href="mailto:kurtz@zbh.uni-hamburg.de"> | |
814 | Stefan Kurtz</a>. Last update: 2017-06-15 | |
815 | </div> | |
816 | } | |
817 | ||
818 | \HCode{ | |
819 | <!--delete paragraph--> | |
820 | <!-- Piwik --> | |
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825 | </script><script type="text/javascript"> | |
826 | try { | |
827 | var piwikTracker = Piwik.getTracker(pkBaseURL + "piwik.php", 3); | |
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830 | } catch( err ) {} | |
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832 | <br/> | |
833 | <noscript> | |
834 | <img src="https://zenlicensemanager.com/piwik/piwik.php?idsite=3" style="border:0" alt=""/> | |
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836 | <!-- End Piwik Tracking Tag --> | |
837 | </div> | |
838 | } | |
839 | \end{document} |
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186 | <!ENTITY ucirc "û"> <!-- latin small letter u with circumflex, | |
187 | U+00FB ISOlat1 --> | |
188 | <!ENTITY uuml "ü"> <!-- latin small letter u with diaeresis, | |
189 | U+00FC ISOlat1 --> | |
190 | <!ENTITY yacute "ý"> <!-- latin small letter y with acute, | |
191 | U+00FD ISOlat1 --> | |
192 | <!ENTITY thorn "þ"> <!-- latin small letter thorn, | |
193 | U+00FE ISOlat1 --> | |
194 | <!ENTITY yuml "ÿ"> <!-- latin small letter y with diaeresis, | |
195 | U+00FF ISOlat1 --> |
0 | <!-- Special characters for XHTML --> | |
1 | ||
2 | <!-- Character entity set. Typical invocation: | |
3 | <!ENTITY % HTMLspecial PUBLIC | |
4 | "-//W3C//ENTITIES Special for XHTML//EN" | |
5 | "http://www.w3.org/TR/xhtml1/DTD/xhtml-special.ent"> | |
6 | %HTMLspecial; | |
7 | --> | |
8 | ||
9 | <!-- Portions (C) International Organization for Standardization 1986: | |
10 | Permission to copy in any form is granted for use with | |
11 | conforming SGML systems and applications as defined in | |
12 | ISO 8879, provided this notice is included in all copies. | |
13 | --> | |
14 | ||
15 | <!-- Relevant ISO entity set is given unless names are newly introduced. | |
16 | New names (i.e., not in ISO 8879 list) do not clash with any | |
17 | existing ISO 8879 entity names. ISO 10646 character numbers | |
18 | are given for each character, in hex. values are decimal | |
19 | conversions of the ISO 10646 values and refer to the document | |
20 | character set. Names are Unicode names. | |
21 | --> | |
22 | ||
23 | <!-- C0 Controls and Basic Latin --> | |
24 | <!ENTITY quot """> <!-- quotation mark, U+0022 ISOnum --> | |
25 | <!ENTITY amp "&#38;"> <!-- ampersand, U+0026 ISOnum --> | |
26 | <!ENTITY lt "&#60;"> <!-- less-than sign, U+003C ISOnum --> | |
27 | <!ENTITY gt ">"> <!-- greater-than sign, U+003E ISOnum --> | |
28 | <!ENTITY apos "'"> <!-- apostrophe = APL quote, U+0027 ISOnum --> | |
29 | ||
30 | <!-- Latin Extended-A --> | |
31 | <!ENTITY OElig "Œ"> <!-- latin capital ligature OE, | |
32 | U+0152 ISOlat2 --> | |
33 | <!ENTITY oelig "œ"> <!-- latin small ligature oe, U+0153 ISOlat2 --> | |
34 | <!-- ligature is a misnomer, this is a separate character in some languages --> | |
35 | <!ENTITY Scaron "Š"> <!-- latin capital letter S with caron, | |
36 | U+0160 ISOlat2 --> | |
37 | <!ENTITY scaron "š"> <!-- latin small letter s with caron, | |
38 | U+0161 ISOlat2 --> | |
39 | <!ENTITY Yuml "Ÿ"> <!-- latin capital letter Y with diaeresis, | |
40 | U+0178 ISOlat2 --> | |
41 | ||
42 | <!-- Spacing Modifier Letters --> | |
43 | <!ENTITY circ "ˆ"> <!-- modifier letter circumflex accent, | |
44 | U+02C6 ISOpub --> | |
45 | <!ENTITY tilde "˜"> <!-- small tilde, U+02DC ISOdia --> | |
46 | ||
47 | <!-- General Punctuation --> | |
48 | <!ENTITY ensp " "> <!-- en space, U+2002 ISOpub --> | |
49 | <!ENTITY emsp " "> <!-- em space, U+2003 ISOpub --> | |
50 | <!ENTITY thinsp " "> <!-- thin space, U+2009 ISOpub --> | |
51 | <!ENTITY zwnj "‌"> <!-- zero width non-joiner, | |
52 | U+200C NEW RFC 2070 --> | |
53 | <!ENTITY zwj "‍"> <!-- zero width joiner, U+200D NEW RFC 2070 --> | |
54 | <!ENTITY lrm "‎"> <!-- left-to-right mark, U+200E NEW RFC 2070 --> | |
55 | <!ENTITY rlm "‏"> <!-- right-to-left mark, U+200F NEW RFC 2070 --> | |
56 | <!ENTITY ndash "–"> <!-- en dash, U+2013 ISOpub --> | |
57 | <!ENTITY mdash "—"> <!-- em dash, U+2014 ISOpub --> | |
58 | <!ENTITY lsquo "‘"> <!-- left single quotation mark, | |
59 | U+2018 ISOnum --> | |
60 | <!ENTITY rsquo "’"> <!-- right single quotation mark, | |
61 | U+2019 ISOnum --> | |
62 | <!ENTITY sbquo "‚"> <!-- single low-9 quotation mark, U+201A NEW --> | |
63 | <!ENTITY ldquo "“"> <!-- left double quotation mark, | |
64 | U+201C ISOnum --> | |
65 | <!ENTITY rdquo "”"> <!-- right double quotation mark, | |
66 | U+201D ISOnum --> | |
67 | <!ENTITY bdquo "„"> <!-- double low-9 quotation mark, U+201E NEW --> | |
68 | <!ENTITY dagger "†"> <!-- dagger, U+2020 ISOpub --> | |
69 | <!ENTITY Dagger "‡"> <!-- double dagger, U+2021 ISOpub --> | |
70 | <!ENTITY permil "‰"> <!-- per mille sign, U+2030 ISOtech --> | |
71 | <!ENTITY lsaquo "‹"> <!-- single left-pointing angle quotation mark, | |
72 | U+2039 ISO proposed --> | |
73 | <!-- lsaquo is proposed but not yet ISO standardized --> | |
74 | <!ENTITY rsaquo "›"> <!-- single right-pointing angle quotation mark, | |
75 | U+203A ISO proposed --> | |
76 | <!-- rsaquo is proposed but not yet ISO standardized --> | |
77 | ||
78 | <!-- Currency Symbols --> | |
79 | <!ENTITY euro "€"> <!-- euro sign, U+20AC NEW --> |
0 | <!-- Mathematical, Greek and Symbolic characters for XHTML --> | |
1 | ||
2 | <!-- Character entity set. Typical invocation: | |
3 | <!ENTITY % HTMLsymbol PUBLIC | |
4 | "-//W3C//ENTITIES Symbols for XHTML//EN" | |
5 | "http://www.w3.org/TR/xhtml1/DTD/xhtml-symbol.ent"> | |
6 | %HTMLsymbol; | |
7 | --> | |
8 | ||
9 | <!-- Portions (C) International Organization for Standardization 1986: | |
10 | Permission to copy in any form is granted for use with | |
11 | conforming SGML systems and applications as defined in | |
12 | ISO 8879, provided this notice is included in all copies. | |
13 | --> | |
14 | ||
15 | <!-- Relevant ISO entity set is given unless names are newly introduced. | |
16 | New names (i.e., not in ISO 8879 list) do not clash with any | |
17 | existing ISO 8879 entity names. ISO 10646 character numbers | |
18 | are given for each character, in hex. values are decimal | |
19 | conversions of the ISO 10646 values and refer to the document | |
20 | character set. Names are Unicode names. | |
21 | --> | |
22 | ||
23 | <!-- Latin Extended-B --> | |
24 | <!ENTITY fnof "ƒ"> <!-- latin small letter f with hook = function | |
25 | = florin, U+0192 ISOtech --> | |
26 | ||
27 | <!-- Greek --> | |
28 | <!ENTITY Alpha "Α"> <!-- greek capital letter alpha, U+0391 --> | |
29 | <!ENTITY Beta "Β"> <!-- greek capital letter beta, U+0392 --> | |
30 | <!ENTITY Gamma "Γ"> <!-- greek capital letter gamma, | |
31 | U+0393 ISOgrk3 --> | |
32 | <!ENTITY Delta "Δ"> <!-- greek capital letter delta, | |
33 | U+0394 ISOgrk3 --> | |
34 | <!ENTITY Epsilon "Ε"> <!-- greek capital letter epsilon, U+0395 --> | |
35 | <!ENTITY Zeta "Ζ"> <!-- greek capital letter zeta, U+0396 --> | |
36 | <!ENTITY Eta "Η"> <!-- greek capital letter eta, U+0397 --> | |
37 | <!ENTITY Theta "Θ"> <!-- greek capital letter theta, | |
38 | U+0398 ISOgrk3 --> | |
39 | <!ENTITY Iota "Ι"> <!-- greek capital letter iota, U+0399 --> | |
40 | <!ENTITY Kappa "Κ"> <!-- greek capital letter kappa, U+039A --> | |
41 | <!ENTITY Lambda "Λ"> <!-- greek capital letter lamda, | |
42 | U+039B ISOgrk3 --> | |
43 | <!ENTITY Mu "Μ"> <!-- greek capital letter mu, U+039C --> | |
44 | <!ENTITY Nu "Ν"> <!-- greek capital letter nu, U+039D --> | |
45 | <!ENTITY Xi "Ξ"> <!-- greek capital letter xi, U+039E ISOgrk3 --> | |
46 | <!ENTITY Omicron "Ο"> <!-- greek capital letter omicron, U+039F --> | |
47 | <!ENTITY Pi "Π"> <!-- greek capital letter pi, U+03A0 ISOgrk3 --> | |
48 | <!ENTITY Rho "Ρ"> <!-- greek capital letter rho, U+03A1 --> | |
49 | <!-- there is no Sigmaf, and no U+03A2 character either --> | |
50 | <!ENTITY Sigma "Σ"> <!-- greek capital letter sigma, | |
51 | U+03A3 ISOgrk3 --> | |
52 | <!ENTITY Tau "Τ"> <!-- greek capital letter tau, U+03A4 --> | |
53 | <!ENTITY Upsilon "Υ"> <!-- greek capital letter upsilon, | |
54 | U+03A5 ISOgrk3 --> | |
55 | <!ENTITY Phi "Φ"> <!-- greek capital letter phi, | |
56 | U+03A6 ISOgrk3 --> | |
57 | <!ENTITY Chi "Χ"> <!-- greek capital letter chi, U+03A7 --> | |
58 | <!ENTITY Psi "Ψ"> <!-- greek capital letter psi, | |
59 | U+03A8 ISOgrk3 --> | |
60 | <!ENTITY Omega "Ω"> <!-- greek capital letter omega, | |
61 | U+03A9 ISOgrk3 --> | |
62 | ||
63 | <!ENTITY alpha "α"> <!-- greek small letter alpha, | |
64 | U+03B1 ISOgrk3 --> | |
65 | <!ENTITY beta "β"> <!-- greek small letter beta, U+03B2 ISOgrk3 --> | |
66 | <!ENTITY gamma "γ"> <!-- greek small letter gamma, | |
67 | U+03B3 ISOgrk3 --> | |
68 | <!ENTITY delta "δ"> <!-- greek small letter delta, | |
69 | U+03B4 ISOgrk3 --> | |
70 | <!ENTITY epsilon "ε"> <!-- greek small letter epsilon, | |
71 | U+03B5 ISOgrk3 --> | |
72 | <!ENTITY zeta "ζ"> <!-- greek small letter zeta, U+03B6 ISOgrk3 --> | |
73 | <!ENTITY eta "η"> <!-- greek small letter eta, U+03B7 ISOgrk3 --> | |
74 | <!ENTITY theta "θ"> <!-- greek small letter theta, | |
75 | U+03B8 ISOgrk3 --> | |
76 | <!ENTITY iota "ι"> <!-- greek small letter iota, U+03B9 ISOgrk3 --> | |
77 | <!ENTITY kappa "κ"> <!-- greek small letter kappa, | |
78 | U+03BA ISOgrk3 --> | |
79 | <!ENTITY lambda "λ"> <!-- greek small letter lamda, | |
80 | U+03BB ISOgrk3 --> | |
81 | <!ENTITY mu "μ"> <!-- greek small letter mu, U+03BC ISOgrk3 --> | |
82 | <!ENTITY nu "ν"> <!-- greek small letter nu, U+03BD ISOgrk3 --> | |
83 | <!ENTITY xi "ξ"> <!-- greek small letter xi, U+03BE ISOgrk3 --> | |
84 | <!ENTITY omicron "ο"> <!-- greek small letter omicron, U+03BF NEW --> | |
85 | <!ENTITY pi "π"> <!-- greek small letter pi, U+03C0 ISOgrk3 --> | |
86 | <!ENTITY rho "ρ"> <!-- greek small letter rho, U+03C1 ISOgrk3 --> | |
87 | <!ENTITY sigmaf "ς"> <!-- greek small letter final sigma, | |
88 | U+03C2 ISOgrk3 --> | |
89 | <!ENTITY sigma "σ"> <!-- greek small letter sigma, | |
90 | U+03C3 ISOgrk3 --> | |
91 | <!ENTITY tau "τ"> <!-- greek small letter tau, U+03C4 ISOgrk3 --> | |
92 | <!ENTITY upsilon "υ"> <!-- greek small letter upsilon, | |
93 | U+03C5 ISOgrk3 --> | |
94 | <!ENTITY phi "φ"> <!-- greek small letter phi, U+03C6 ISOgrk3 --> | |
95 | <!ENTITY chi "χ"> <!-- greek small letter chi, U+03C7 ISOgrk3 --> | |
96 | <!ENTITY psi "ψ"> <!-- greek small letter psi, U+03C8 ISOgrk3 --> | |
97 | <!ENTITY omega "ω"> <!-- greek small letter omega, | |
98 | U+03C9 ISOgrk3 --> | |
99 | <!ENTITY thetasym "ϑ"> <!-- greek theta symbol, | |
100 | U+03D1 NEW --> | |
101 | <!ENTITY upsih "ϒ"> <!-- greek upsilon with hook symbol, | |
102 | U+03D2 NEW --> | |
103 | <!ENTITY piv "ϖ"> <!-- greek pi symbol, U+03D6 ISOgrk3 --> | |
104 | ||
105 | <!-- General Punctuation --> | |
106 | <!ENTITY bull "•"> <!-- bullet = black small circle, | |
107 | U+2022 ISOpub --> | |
108 | <!-- bullet is NOT the same as bullet operator, U+2219 --> | |
109 | <!ENTITY hellip "…"> <!-- horizontal ellipsis = three dot leader, | |
110 | U+2026 ISOpub --> | |
111 | <!ENTITY prime "′"> <!-- prime = minutes = feet, U+2032 ISOtech --> | |
112 | <!ENTITY Prime "″"> <!-- double prime = seconds = inches, | |
113 | U+2033 ISOtech --> | |
114 | <!ENTITY oline "‾"> <!-- overline = spacing overscore, | |
115 | U+203E NEW --> | |
116 | <!ENTITY frasl "⁄"> <!-- fraction slash, U+2044 NEW --> | |
117 | ||
118 | <!-- Letterlike Symbols --> | |
119 | <!ENTITY weierp "℘"> <!-- script capital P = power set | |
120 | = Weierstrass p, U+2118 ISOamso --> | |
121 | <!ENTITY image "ℑ"> <!-- black-letter capital I = imaginary part, | |
122 | U+2111 ISOamso --> | |
123 | <!ENTITY real "ℜ"> <!-- black-letter capital R = real part symbol, | |
124 | U+211C ISOamso --> | |
125 | <!ENTITY trade "™"> <!-- trade mark sign, U+2122 ISOnum --> | |
126 | <!ENTITY alefsym "ℵ"> <!-- alef symbol = first transfinite cardinal, | |
127 | U+2135 NEW --> | |
128 | <!-- alef symbol is NOT the same as hebrew letter alef, | |
129 | U+05D0 although the same glyph could be used to depict both characters --> | |
130 | ||
131 | <!-- Arrows --> | |
132 | <!ENTITY larr "←"> <!-- leftwards arrow, U+2190 ISOnum --> | |
133 | <!ENTITY uarr "↑"> <!-- upwards arrow, U+2191 ISOnum--> | |
134 | <!ENTITY rarr "→"> <!-- rightwards arrow, U+2192 ISOnum --> | |
135 | <!ENTITY darr "↓"> <!-- downwards arrow, U+2193 ISOnum --> | |
136 | <!ENTITY harr "↔"> <!-- left right arrow, U+2194 ISOamsa --> | |
137 | <!ENTITY crarr "↵"> <!-- downwards arrow with corner leftwards | |
138 | = carriage return, U+21B5 NEW --> | |
139 | <!ENTITY lArr "⇐"> <!-- leftwards double arrow, U+21D0 ISOtech --> | |
140 | <!-- Unicode does not say that lArr is the same as the 'is implied by' arrow | |
141 | but also does not have any other character for that function. So lArr can | |
142 | be used for 'is implied by' as ISOtech suggests --> | |
143 | <!ENTITY uArr "⇑"> <!-- upwards double arrow, U+21D1 ISOamsa --> | |
144 | <!ENTITY rArr "⇒"> <!-- rightwards double arrow, | |
145 | U+21D2 ISOtech --> | |
146 | <!-- Unicode does not say this is the 'implies' character but does not have | |
147 | another character with this function so rArr can be used for 'implies' | |
148 | as ISOtech suggests --> | |
149 | <!ENTITY dArr "⇓"> <!-- downwards double arrow, U+21D3 ISOamsa --> | |
150 | <!ENTITY hArr "⇔"> <!-- left right double arrow, | |
151 | U+21D4 ISOamsa --> | |
152 | ||
153 | <!-- Mathematical Operators --> | |
154 | <!ENTITY forall "∀"> <!-- for all, U+2200 ISOtech --> | |
155 | <!ENTITY part "∂"> <!-- partial differential, U+2202 ISOtech --> | |
156 | <!ENTITY exist "∃"> <!-- there exists, U+2203 ISOtech --> | |
157 | <!ENTITY empty "∅"> <!-- empty set = null set, U+2205 ISOamso --> | |
158 | <!ENTITY nabla "∇"> <!-- nabla = backward difference, | |
159 | U+2207 ISOtech --> | |
160 | <!ENTITY isin "∈"> <!-- element of, U+2208 ISOtech --> | |
161 | <!ENTITY notin "∉"> <!-- not an element of, U+2209 ISOtech --> | |
162 | <!ENTITY ni "∋"> <!-- contains as member, U+220B ISOtech --> | |
163 | <!ENTITY prod "∏"> <!-- n-ary product = product sign, | |
164 | U+220F ISOamsb --> | |
165 | <!-- prod is NOT the same character as U+03A0 'greek capital letter pi' though | |
166 | the same glyph might be used for both --> | |
167 | <!ENTITY sum "∑"> <!-- n-ary summation, U+2211 ISOamsb --> | |
168 | <!-- sum is NOT the same character as U+03A3 'greek capital letter sigma' | |
169 | though the same glyph might be used for both --> | |
170 | <!ENTITY minus "−"> <!-- minus sign, U+2212 ISOtech --> | |
171 | <!ENTITY lowast "∗"> <!-- asterisk operator, U+2217 ISOtech --> | |
172 | <!ENTITY radic "√"> <!-- square root = radical sign, | |
173 | U+221A ISOtech --> | |
174 | <!ENTITY prop "∝"> <!-- proportional to, U+221D ISOtech --> | |
175 | <!ENTITY infin "∞"> <!-- infinity, U+221E ISOtech --> | |
176 | <!ENTITY ang "∠"> <!-- angle, U+2220 ISOamso --> | |
177 | <!ENTITY and "∧"> <!-- logical and = wedge, U+2227 ISOtech --> | |
178 | <!ENTITY or "∨"> <!-- logical or = vee, U+2228 ISOtech --> | |
179 | <!ENTITY cap "∩"> <!-- intersection = cap, U+2229 ISOtech --> | |
180 | <!ENTITY cup "∪"> <!-- union = cup, U+222A ISOtech --> | |
181 | <!ENTITY int "∫"> <!-- integral, U+222B ISOtech --> | |
182 | <!ENTITY there4 "∴"> <!-- therefore, U+2234 ISOtech --> | |
183 | <!ENTITY sim "∼"> <!-- tilde operator = varies with = similar to, | |
184 | U+223C ISOtech --> | |
185 | <!-- tilde operator is NOT the same character as the tilde, U+007E, | |
186 | although the same glyph might be used to represent both --> | |
187 | <!ENTITY cong "≅"> <!-- approximately equal to, U+2245 ISOtech --> | |
188 | <!ENTITY asymp "≈"> <!-- almost equal to = asymptotic to, | |
189 | U+2248 ISOamsr --> | |
190 | <!ENTITY ne "≠"> <!-- not equal to, U+2260 ISOtech --> | |
191 | <!ENTITY equiv "≡"> <!-- identical to, U+2261 ISOtech --> | |
192 | <!ENTITY le "≤"> <!-- less-than or equal to, U+2264 ISOtech --> | |
193 | <!ENTITY ge "≥"> <!-- greater-than or equal to, | |
194 | U+2265 ISOtech --> | |
195 | <!ENTITY sub "⊂"> <!-- subset of, U+2282 ISOtech --> | |
196 | <!ENTITY sup "⊃"> <!-- superset of, U+2283 ISOtech --> | |
197 | <!ENTITY nsub "⊄"> <!-- not a subset of, U+2284 ISOamsn --> | |
198 | <!ENTITY sube "⊆"> <!-- subset of or equal to, U+2286 ISOtech --> | |
199 | <!ENTITY supe "⊇"> <!-- superset of or equal to, | |
200 | U+2287 ISOtech --> | |
201 | <!ENTITY oplus "⊕"> <!-- circled plus = direct sum, | |
202 | U+2295 ISOamsb --> | |
203 | <!ENTITY otimes "⊗"> <!-- circled times = vector product, | |
204 | U+2297 ISOamsb --> | |
205 | <!ENTITY perp "⊥"> <!-- up tack = orthogonal to = perpendicular, | |
206 | U+22A5 ISOtech --> | |
207 | <!ENTITY sdot "⋅"> <!-- dot operator, U+22C5 ISOamsb --> | |
208 | <!-- dot operator is NOT the same character as U+00B7 middle dot --> | |
209 | ||
210 | <!-- Miscellaneous Technical --> | |
211 | <!ENTITY lceil "⌈"> <!-- left ceiling = APL upstile, | |
212 | U+2308 ISOamsc --> | |
213 | <!ENTITY rceil "⌉"> <!-- right ceiling, U+2309 ISOamsc --> | |
214 | <!ENTITY lfloor "⌊"> <!-- left floor = APL downstile, | |
215 | U+230A ISOamsc --> | |
216 | <!ENTITY rfloor "⌋"> <!-- right floor, U+230B ISOamsc --> | |
217 | <!ENTITY lang "〈"> <!-- left-pointing angle bracket = bra, | |
218 | U+2329 ISOtech --> | |
219 | <!-- lang is NOT the same character as U+003C 'less than sign' | |
220 | or U+2039 'single left-pointing angle quotation mark' --> | |
221 | <!ENTITY rang "〉"> <!-- right-pointing angle bracket = ket, | |
222 | U+232A ISOtech --> | |
223 | <!-- rang is NOT the same character as U+003E 'greater than sign' | |
224 | or U+203A 'single right-pointing angle quotation mark' --> | |
225 | ||
226 | <!-- Geometric Shapes --> | |
227 | <!ENTITY loz "◊"> <!-- lozenge, U+25CA ISOpub --> | |
228 | ||
229 | <!-- Miscellaneous Symbols --> | |
230 | <!ENTITY spades "♠"> <!-- black spade suit, U+2660 ISOpub --> | |
231 | <!-- black here seems to mean filled as opposed to hollow --> | |
232 | <!ENTITY clubs "♣"> <!-- black club suit = shamrock, | |
233 | U+2663 ISOpub --> | |
234 | <!ENTITY hearts "♥"> <!-- black heart suit = valentine, | |
235 | U+2665 ISOpub --> | |
236 | <!ENTITY diams "♦"> <!-- black diamond suit, U+2666 ISOpub --> |
0 | <!-- | |
1 | Extensible HTML version 1.0 Transitional DTD | |
2 | ||
3 | This is the same as HTML 4 Transitional except for | |
4 | changes due to the differences between XML and SGML. | |
5 | ||
6 | Namespace = http://www.w3.org/1999/xhtml | |
7 | ||
8 | For further information, see: http://www.w3.org/TR/xhtml1 | |
9 | ||
10 | Copyright (c) 1998-2002 W3C (MIT, INRIA, Keio), | |
11 | All Rights Reserved. | |
12 | ||
13 | This DTD module is identified by the PUBLIC and SYSTEM identifiers: | |
14 | ||
15 | PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" | |
16 | SYSTEM "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd" | |
17 | ||
18 | $Revision: 1.2 $ | |
19 | $Date: 2002/08/01 18:37:55 $ | |
20 | ||
21 | --> | |
22 | ||
23 | <!--================ Character mnemonic entities =========================--> | |
24 | ||
25 | <!ENTITY % HTMLlat1 PUBLIC | |
26 | "-//W3C//ENTITIES Latin 1 for XHTML//EN" | |
27 | "xhtml-lat1.ent"> | |
28 | %HTMLlat1; | |
29 | ||
30 | <!ENTITY % HTMLsymbol PUBLIC | |
31 | "-//W3C//ENTITIES Symbols for XHTML//EN" | |
32 | "xhtml-symbol.ent"> | |
33 | %HTMLsymbol; | |
34 | ||
35 | <!ENTITY % HTMLspecial PUBLIC | |
36 | "-//W3C//ENTITIES Special for XHTML//EN" | |
37 | "xhtml-special.ent"> | |
38 | %HTMLspecial; | |
39 | ||
40 | <!--================== Imported Names ====================================--> | |
41 | ||
42 | <!ENTITY % ContentType "CDATA"> | |
43 | <!-- media type, as per [RFC2045] --> | |
44 | ||
45 | <!ENTITY % ContentTypes "CDATA"> | |
46 | <!-- comma-separated list of media types, as per [RFC2045] --> | |
47 | ||
48 | <!ENTITY % Charset "CDATA"> | |
49 | <!-- a character encoding, as per [RFC2045] --> | |
50 | ||
51 | <!ENTITY % Charsets "CDATA"> | |
52 | <!-- a space separated list of character encodings, as per [RFC2045] --> | |
53 | ||
54 | <!ENTITY % LanguageCode "NMTOKEN"> | |
55 | <!-- a language code, as per [RFC3066] --> | |
56 | ||
57 | <!ENTITY % Character "CDATA"> | |
58 | <!-- a single character, as per section 2.2 of [XML] --> | |
59 | ||
60 | <!ENTITY % Number "CDATA"> | |
61 | <!-- one or more digits --> | |
62 | ||
63 | <!ENTITY % LinkTypes "CDATA"> | |
64 | <!-- space-separated list of link types --> | |
65 | ||
66 | <!ENTITY % MediaDesc "CDATA"> | |
67 | <!-- single or comma-separated list of media descriptors --> | |
68 | ||
69 | <!ENTITY % URI "CDATA"> | |
70 | <!-- a Uniform Resource Identifier, see [RFC2396] --> | |
71 | ||
72 | <!ENTITY % UriList "CDATA"> | |
73 | <!-- a space separated list of Uniform Resource Identifiers --> | |
74 | ||
75 | <!ENTITY % Datetime "CDATA"> | |
76 | <!-- date and time information. ISO date format --> | |
77 | ||
78 | <!ENTITY % Script "CDATA"> | |
79 | <!-- script expression --> | |
80 | ||
81 | <!ENTITY % StyleSheet "CDATA"> | |
82 | <!-- style sheet data --> | |
83 | ||
84 | <!ENTITY % Text "CDATA"> | |
85 | <!-- used for titles etc. --> | |
86 | ||
87 | <!ENTITY % FrameTarget "NMTOKEN"> | |
88 | <!-- render in this frame --> | |
89 | ||
90 | <!ENTITY % Length "CDATA"> | |
91 | <!-- nn for pixels or nn% for percentage length --> | |
92 | ||
93 | <!ENTITY % MultiLength "CDATA"> | |
94 | <!-- pixel, percentage, or relative --> | |
95 | ||
96 | <!ENTITY % Pixels "CDATA"> | |
97 | <!-- integer representing length in pixels --> | |
98 | ||
99 | <!-- these are used for image maps --> | |
100 | ||
101 | <!ENTITY % Shape "(rect|circle|poly|default)"> | |
102 | ||
103 | <!ENTITY % Coords "CDATA"> | |
104 | <!-- comma separated list of lengths --> | |
105 | ||
106 | <!-- used for object, applet, img, input and iframe --> | |
107 | <!ENTITY % ImgAlign "(top|middle|bottom|left|right)"> | |
108 | ||
109 | <!-- a color using sRGB: #RRGGBB as Hex values --> | |
110 | <!ENTITY % Color "CDATA"> | |
111 | ||
112 | <!-- There are also 16 widely known color names with their sRGB values: | |
113 | ||
114 | Black = #000000 Green = #008000 | |
115 | Silver = #C0C0C0 Lime = #00FF00 | |
116 | Gray = #808080 Olive = #808000 | |
117 | White = #FFFFFF Yellow = #FFFF00 | |
118 | Maroon = #800000 Navy = #000080 | |
119 | Red = #FF0000 Blue = #0000FF | |
120 | Purple = #800080 Teal = #008080 | |
121 | Fuchsia= #FF00FF Aqua = #00FFFF | |
122 | --> | |
123 | ||
124 | <!--=================== Generic Attributes ===============================--> | |
125 | ||
126 | <!-- core attributes common to most elements | |
127 | id document-wide unique id | |
128 | class space separated list of classes | |
129 | style associated style info | |
130 | title advisory title/amplification | |
131 | --> | |
132 | <!ENTITY % coreattrs | |
133 | "id ID #IMPLIED | |
134 | class CDATA #IMPLIED | |
135 | style %StyleSheet; #IMPLIED | |
136 | title %Text; #IMPLIED" | |
137 | > | |
138 | ||
139 | <!-- internationalization attributes | |
140 | lang language code (backwards compatible) | |
141 | xml:lang language code (as per XML 1.0 spec) | |
142 | dir direction for weak/neutral text | |
143 | --> | |
144 | <!ENTITY % i18n | |
145 | "lang %LanguageCode; #IMPLIED | |
146 | xml:lang %LanguageCode; #IMPLIED | |
147 | dir (ltr|rtl) #IMPLIED" | |
148 | > | |
149 | ||
150 | <!-- attributes for common UI events | |
151 | onclick a pointer button was clicked | |
152 | ondblclick a pointer button was double clicked | |
153 | onmousedown a pointer button was pressed down | |
154 | onmouseup a pointer button was released | |
155 | onmousemove a pointer was moved onto the element | |
156 | onmouseout a pointer was moved away from the element | |
157 | onkeypress a key was pressed and released | |
158 | onkeydown a key was pressed down | |
159 | onkeyup a key was released | |
160 | --> | |
161 | <!ENTITY % events | |
162 | "onclick %Script; #IMPLIED | |
163 | ondblclick %Script; #IMPLIED | |
164 | onmousedown %Script; #IMPLIED | |
165 | onmouseup %Script; #IMPLIED | |
166 | onmouseover %Script; #IMPLIED | |
167 | onmousemove %Script; #IMPLIED | |
168 | onmouseout %Script; #IMPLIED | |
169 | onkeypress %Script; #IMPLIED | |
170 | onkeydown %Script; #IMPLIED | |
171 | onkeyup %Script; #IMPLIED" | |
172 | > | |
173 | ||
174 | <!-- attributes for elements that can get the focus | |
175 | accesskey accessibility key character | |
176 | tabindex position in tabbing order | |
177 | onfocus the element got the focus | |
178 | onblur the element lost the focus | |
179 | --> | |
180 | <!ENTITY % focus | |
181 | "accesskey %Character; #IMPLIED | |
182 | tabindex %Number; #IMPLIED | |
183 | onfocus %Script; #IMPLIED | |
184 | onblur %Script; #IMPLIED" | |
185 | > | |
186 | ||
187 | <!ENTITY % attrs "%coreattrs; %i18n; %events;"> | |
188 | ||
189 | <!-- text alignment for p, div, h1-h6. The default is | |
190 | align="left" for ltr headings, "right" for rtl --> | |
191 | ||
192 | <!ENTITY % TextAlign "align (left|center|right|justify) #IMPLIED"> | |
193 | ||
194 | <!--=================== Text Elements ====================================--> | |
195 | ||
196 | <!ENTITY % special.extra | |
197 | "object | applet | img | map | iframe"> | |
198 | ||
199 | <!ENTITY % special.basic | |
200 | "br | span | bdo"> | |
201 | ||
202 | <!ENTITY % special | |
203 | "%special.basic; | %special.extra;"> | |
204 | ||
205 | <!ENTITY % fontstyle.extra "big | small | font | basefont"> | |
206 | ||
207 | <!ENTITY % fontstyle.basic "tt | i | b | u | |
208 | | s | strike "> | |
209 | ||
210 | <!ENTITY % fontstyle "%fontstyle.basic; | %fontstyle.extra;"> | |
211 | ||
212 | <!ENTITY % phrase.extra "sub | sup"> | |
213 | <!ENTITY % phrase.basic "em | strong | dfn | code | q | | |
214 | samp | kbd | var | cite | abbr | acronym"> | |
215 | ||
216 | <!ENTITY % phrase "%phrase.basic; | %phrase.extra;"> | |
217 | ||
218 | <!ENTITY % inline.forms "input | select | textarea | label | button"> | |
219 | ||
220 | <!-- these can occur at block or inline level --> | |
221 | <!ENTITY % misc.inline "ins | del | script"> | |
222 | ||
223 | <!-- these can only occur at block level --> | |
224 | <!ENTITY % misc "noscript | %misc.inline;"> | |
225 | ||
226 | <!ENTITY % inline "a | %special; | %fontstyle; | %phrase; | %inline.forms;"> | |
227 | ||
228 | <!-- %Inline; covers inline or "text-level" elements --> | |
229 | <!ENTITY % Inline "(#PCDATA | %inline; | %misc.inline;)*"> | |
230 | ||
231 | <!--================== Block level elements ==============================--> | |
232 | ||
233 | <!ENTITY % heading "h1|h2|h3|h4|h5|h6"> | |
234 | <!ENTITY % lists "ul | ol | dl | menu | dir"> | |
235 | <!ENTITY % blocktext "pre | hr | blockquote | address | center | noframes"> | |
236 | ||
237 | <!ENTITY % block | |
238 | "p | %heading; | div | %lists; | %blocktext; | isindex |fieldset | table"> | |
239 | ||
240 | <!-- %Flow; mixes block and inline and is used for list items etc. --> | |
241 | <!ENTITY % Flow "(#PCDATA | %block; | form | %inline; | %misc;)*"> | |
242 | ||
243 | <!--================== Content models for exclusions =====================--> | |
244 | ||
245 | <!-- a elements use %Inline; excluding a --> | |
246 | ||
247 | <!ENTITY % a.content | |
248 | "(#PCDATA | %special; | %fontstyle; | %phrase; | %inline.forms; | %misc.inline;)*"> | |
249 | ||
250 | <!-- pre uses %Inline excluding img, object, applet, big, small, | |
251 | font, or basefont --> | |
252 | ||
253 | <!ENTITY % pre.content | |
254 | "(#PCDATA | a | %special.basic; | %fontstyle.basic; | %phrase.basic; | | |
255 | %inline.forms; | %misc.inline;)*"> | |
256 | ||
257 | <!-- form uses %Flow; excluding form --> | |
258 | ||
259 | <!ENTITY % form.content "(#PCDATA | %block; | %inline; | %misc;)*"> | |
260 | ||
261 | <!-- button uses %Flow; but excludes a, form, form controls, iframe --> | |
262 | ||
263 | <!ENTITY % button.content | |
264 | "(#PCDATA | p | %heading; | div | %lists; | %blocktext; | | |
265 | table | br | span | bdo | object | applet | img | map | | |
266 | %fontstyle; | %phrase; | %misc;)*"> | |
267 | ||
268 | <!--================ Document Structure ==================================--> | |
269 | ||
270 | <!-- the namespace URI designates the document profile --> | |
271 | ||
272 | <!ELEMENT html (head, body)> | |
273 | <!ATTLIST html | |
274 | %i18n; | |
275 | id ID #IMPLIED | |
276 | xmlns %URI; #FIXED 'http://www.w3.org/1999/xhtml' | |
277 | > | |
278 | ||
279 | <!--================ Document Head =======================================--> | |
280 | ||
281 | <!ENTITY % head.misc "(script|style|meta|link|object|isindex)*"> | |
282 | ||
283 | <!-- content model is %head.misc; combined with a single | |
284 | title and an optional base element in any order --> | |
285 | ||
286 | <!ELEMENT head (%head.misc;, | |
287 | ((title, %head.misc;, (base, %head.misc;)?) | | |
288 | (base, %head.misc;, (title, %head.misc;))))> | |
289 | ||
290 | <!ATTLIST head | |
291 | %i18n; | |
292 | id ID #IMPLIED | |
293 | profile %URI; #IMPLIED | |
294 | > | |
295 | ||
296 | <!-- The title element is not considered part of the flow of text. | |
297 | It should be displayed, for example as the page header or | |
298 | window title. Exactly one title is required per document. | |
299 | --> | |
300 | <!ELEMENT title (#PCDATA)> | |
301 | <!ATTLIST title | |
302 | %i18n; | |
303 | id ID #IMPLIED | |
304 | > | |
305 | ||
306 | <!-- document base URI --> | |
307 | ||
308 | <!ELEMENT base EMPTY> | |
309 | <!ATTLIST base | |
310 | id ID #IMPLIED | |
311 | href %URI; #IMPLIED | |
312 | target %FrameTarget; #IMPLIED | |
313 | > | |
314 | ||
315 | <!-- generic metainformation --> | |
316 | <!ELEMENT meta EMPTY> | |
317 | <!ATTLIST meta | |
318 | %i18n; | |
319 | id ID #IMPLIED | |
320 | http-equiv CDATA #IMPLIED | |
321 | name CDATA #IMPLIED | |
322 | content CDATA #REQUIRED | |
323 | scheme CDATA #IMPLIED | |
324 | > | |
325 | ||
326 | <!-- | |
327 | Relationship values can be used in principle: | |
328 | ||
329 | a) for document specific toolbars/menus when used | |
330 | with the link element in document head e.g. | |
331 | start, contents, previous, next, index, end, help | |
332 | b) to link to a separate style sheet (rel="stylesheet") | |
333 | c) to make a link to a script (rel="script") | |
334 | d) by stylesheets to control how collections of | |
335 | html nodes are rendered into printed documents | |
336 | e) to make a link to a printable version of this document | |
337 | e.g. a PostScript or PDF version (rel="alternate" media="print") | |
338 | --> | |
339 | ||
340 | <!ELEMENT link EMPTY> | |
341 | <!ATTLIST link | |
342 | %attrs; | |
343 | charset %Charset; #IMPLIED | |
344 | href %URI; #IMPLIED | |
345 | hreflang %LanguageCode; #IMPLIED | |
346 | type %ContentType; #IMPLIED | |
347 | rel %LinkTypes; #IMPLIED | |
348 | rev %LinkTypes; #IMPLIED | |
349 | media %MediaDesc; #IMPLIED | |
350 | target %FrameTarget; #IMPLIED | |
351 | > | |
352 | ||
353 | <!-- style info, which may include CDATA sections --> | |
354 | <!ELEMENT style (#PCDATA)> | |
355 | <!ATTLIST style | |
356 | %i18n; | |
357 | id ID #IMPLIED | |
358 | type %ContentType; #REQUIRED | |
359 | media %MediaDesc; #IMPLIED | |
360 | title %Text; #IMPLIED | |
361 | xml:space (preserve) #FIXED 'preserve' | |
362 | > | |
363 | ||
364 | <!-- script statements, which may include CDATA sections --> | |
365 | <!ELEMENT script (#PCDATA)> | |
366 | <!ATTLIST script | |
367 | id ID #IMPLIED | |
368 | charset %Charset; #IMPLIED | |
369 | type %ContentType; #REQUIRED | |
370 | language CDATA #IMPLIED | |
371 | src %URI; #IMPLIED | |
372 | defer (defer) #IMPLIED | |
373 | xml:space (preserve) #FIXED 'preserve' | |
374 | > | |
375 | ||
376 | <!-- alternate content container for non script-based rendering --> | |
377 | ||
378 | <!ELEMENT noscript %Flow;> | |
379 | <!ATTLIST noscript | |
380 | %attrs; | |
381 | > | |
382 | ||
383 | <!--======================= Frames =======================================--> | |
384 | ||
385 | <!-- inline subwindow --> | |
386 | ||
387 | <!ELEMENT iframe %Flow;> | |
388 | <!ATTLIST iframe | |
389 | %coreattrs; | |
390 | longdesc %URI; #IMPLIED | |
391 | name NMTOKEN #IMPLIED | |
392 | src %URI; #IMPLIED | |
393 | frameborder (1|0) "1" | |
394 | marginwidth %Pixels; #IMPLIED | |
395 | marginheight %Pixels; #IMPLIED | |
396 | scrolling (yes|no|auto) "auto" | |
397 | align %ImgAlign; #IMPLIED | |
398 | height %Length; #IMPLIED | |
399 | width %Length; #IMPLIED | |
400 | > | |
401 | ||
402 | <!-- alternate content container for non frame-based rendering --> | |
403 | ||
404 | <!ELEMENT noframes %Flow;> | |
405 | <!ATTLIST noframes | |
406 | %attrs; | |
407 | > | |
408 | ||
409 | <!--=================== Document Body ====================================--> | |
410 | ||
411 | <!ELEMENT body %Flow;> | |
412 | <!ATTLIST body | |
413 | %attrs; | |
414 | onload %Script; #IMPLIED | |
415 | onunload %Script; #IMPLIED | |
416 | background %URI; #IMPLIED | |
417 | bgcolor %Color; #IMPLIED | |
418 | text %Color; #IMPLIED | |
419 | link %Color; #IMPLIED | |
420 | vlink %Color; #IMPLIED | |
421 | alink %Color; #IMPLIED | |
422 | > | |
423 | ||
424 | <!ELEMENT div %Flow;> <!-- generic language/style container --> | |
425 | <!ATTLIST div | |
426 | %attrs; | |
427 | %TextAlign; | |
428 | > | |
429 | ||
430 | <!--=================== Paragraphs =======================================--> | |
431 | ||
432 | <!ELEMENT p %Inline;> | |
433 | <!ATTLIST p | |
434 | %attrs; | |
435 | %TextAlign; | |
436 | > | |
437 | ||
438 | <!--=================== Headings =========================================--> | |
439 | ||
440 | <!-- | |
441 | There are six levels of headings from h1 (the most important) | |
442 | to h6 (the least important). | |
443 | --> | |
444 | ||
445 | <!ELEMENT h1 %Inline;> | |
446 | <!ATTLIST h1 | |
447 | %attrs; | |
448 | %TextAlign; | |
449 | > | |
450 | ||
451 | <!ELEMENT h2 %Inline;> | |
452 | <!ATTLIST h2 | |
453 | %attrs; | |
454 | %TextAlign; | |
455 | > | |
456 | ||
457 | <!ELEMENT h3 %Inline;> | |
458 | <!ATTLIST h3 | |
459 | %attrs; | |
460 | %TextAlign; | |
461 | > | |
462 | ||
463 | <!ELEMENT h4 %Inline;> | |
464 | <!ATTLIST h4 | |
465 | %attrs; | |
466 | %TextAlign; | |
467 | > | |
468 | ||
469 | <!ELEMENT h5 %Inline;> | |
470 | <!ATTLIST h5 | |
471 | %attrs; | |
472 | %TextAlign; | |
473 | > | |
474 | ||
475 | <!ELEMENT h6 %Inline;> | |
476 | <!ATTLIST h6 | |
477 | %attrs; | |
478 | %TextAlign; | |
479 | > | |
480 | ||
481 | <!--=================== Lists ============================================--> | |
482 | ||
483 | <!-- Unordered list bullet styles --> | |
484 | ||
485 | <!ENTITY % ULStyle "(disc|square|circle)"> | |
486 | ||
487 | <!-- Unordered list --> | |
488 | ||
489 | <!ELEMENT ul (li)+> | |
490 | <!ATTLIST ul | |
491 | %attrs; | |
492 | type %ULStyle; #IMPLIED | |
493 | compact (compact) #IMPLIED | |
494 | > | |
495 | ||
496 | <!-- Ordered list numbering style | |
497 | ||
498 | 1 arabic numbers 1, 2, 3, ... | |
499 | a lower alpha a, b, c, ... | |
500 | A upper alpha A, B, C, ... | |
501 | i lower roman i, ii, iii, ... | |
502 | I upper roman I, II, III, ... | |
503 | ||
504 | The style is applied to the sequence number which by default | |
505 | is reset to 1 for the first list item in an ordered list. | |
506 | --> | |
507 | <!ENTITY % OLStyle "CDATA"> | |
508 | ||
509 | <!-- Ordered (numbered) list --> | |
510 | ||
511 | <!ELEMENT ol (li)+> | |
512 | <!ATTLIST ol | |
513 | %attrs; | |
514 | type %OLStyle; #IMPLIED | |
515 | compact (compact) #IMPLIED | |
516 | start %Number; #IMPLIED | |
517 | > | |
518 | ||
519 | <!-- single column list (DEPRECATED) --> | |
520 | <!ELEMENT menu (li)+> | |
521 | <!ATTLIST menu | |
522 | %attrs; | |
523 | compact (compact) #IMPLIED | |
524 | > | |
525 | ||
526 | <!-- multiple column list (DEPRECATED) --> | |
527 | <!ELEMENT dir (li)+> | |
528 | <!ATTLIST dir | |
529 | %attrs; | |
530 | compact (compact) #IMPLIED | |
531 | > | |
532 | ||
533 | <!-- LIStyle is constrained to: "(%ULStyle;|%OLStyle;)" --> | |
534 | <!ENTITY % LIStyle "CDATA"> | |
535 | ||
536 | <!-- list item --> | |
537 | ||
538 | <!ELEMENT li %Flow;> | |
539 | <!ATTLIST li | |
540 | %attrs; | |
541 | type %LIStyle; #IMPLIED | |
542 | value %Number; #IMPLIED | |
543 | > | |
544 | ||
545 | <!-- definition lists - dt for term, dd for its definition --> | |
546 | ||
547 | <!ELEMENT dl (dt|dd)+> | |
548 | <!ATTLIST dl | |
549 | %attrs; | |
550 | compact (compact) #IMPLIED | |
551 | > | |
552 | ||
553 | <!ELEMENT dt %Inline;> | |
554 | <!ATTLIST dt | |
555 | %attrs; | |
556 | > | |
557 | ||
558 | <!ELEMENT dd %Flow;> | |
559 | <!ATTLIST dd | |
560 | %attrs; | |
561 | > | |
562 | ||
563 | <!--=================== Address ==========================================--> | |
564 | ||
565 | <!-- information on author --> | |
566 | ||
567 | <!ELEMENT address (#PCDATA | %inline; | %misc.inline; | p)*> | |
568 | <!ATTLIST address | |
569 | %attrs; | |
570 | > | |
571 | ||
572 | <!--=================== Horizontal Rule ==================================--> | |
573 | ||
574 | <!ELEMENT hr EMPTY> | |
575 | <!ATTLIST hr | |
576 | %attrs; | |
577 | align (left|center|right) #IMPLIED | |
578 | noshade (noshade) #IMPLIED | |
579 | size %Pixels; #IMPLIED | |
580 | width %Length; #IMPLIED | |
581 | > | |
582 | ||
583 | <!--=================== Preformatted Text ================================--> | |
584 | ||
585 | <!-- content is %Inline; excluding | |
586 | "img|object|applet|big|small|sub|sup|font|basefont" --> | |
587 | ||
588 | <!ELEMENT pre %pre.content;> | |
589 | <!ATTLIST pre | |
590 | %attrs; | |
591 | width %Number; #IMPLIED | |
592 | xml:space (preserve) #FIXED 'preserve' | |
593 | > | |
594 | ||
595 | <!--=================== Block-like Quotes ================================--> | |
596 | ||
597 | <!ELEMENT blockquote %Flow;> | |
598 | <!ATTLIST blockquote | |
599 | %attrs; | |
600 | cite %URI; #IMPLIED | |
601 | > | |
602 | ||
603 | <!--=================== Text alignment ===================================--> | |
604 | ||
605 | <!-- center content --> | |
606 | <!ELEMENT center %Flow;> | |
607 | <!ATTLIST center | |
608 | %attrs; | |
609 | > | |
610 | ||
611 | <!--=================== Inserted/Deleted Text ============================--> | |
612 | ||
613 | <!-- | |
614 | ins/del are allowed in block and inline content, but its | |
615 | inappropriate to include block content within an ins element | |
616 | occurring in inline content. | |
617 | --> | |
618 | <!ELEMENT ins %Flow;> | |
619 | <!ATTLIST ins | |
620 | %attrs; | |
621 | cite %URI; #IMPLIED | |
622 | datetime %Datetime; #IMPLIED | |
623 | > | |
624 | ||
625 | <!ELEMENT del %Flow;> | |
626 | <!ATTLIST del | |
627 | %attrs; | |
628 | cite %URI; #IMPLIED | |
629 | datetime %Datetime; #IMPLIED | |
630 | > | |
631 | ||
632 | <!--================== The Anchor Element ================================--> | |
633 | ||
634 | <!-- content is %Inline; except that anchors shouldn't be nested --> | |
635 | ||
636 | <!ELEMENT a %a.content;> | |
637 | <!ATTLIST a | |
638 | %attrs; | |
639 | %focus; | |
640 | charset %Charset; #IMPLIED | |
641 | type %ContentType; #IMPLIED | |
642 | name NMTOKEN #IMPLIED | |
643 | href %URI; #IMPLIED | |
644 | hreflang %LanguageCode; #IMPLIED | |
645 | rel %LinkTypes; #IMPLIED | |
646 | rev %LinkTypes; #IMPLIED | |
647 | shape %Shape; "rect" | |
648 | coords %Coords; #IMPLIED | |
649 | target %FrameTarget; #IMPLIED | |
650 | > | |
651 | ||
652 | <!--===================== Inline Elements ================================--> | |
653 | ||
654 | <!ELEMENT span %Inline;> <!-- generic language/style container --> | |
655 | <!ATTLIST span | |
656 | %attrs; | |
657 | > | |
658 | ||
659 | <!ELEMENT bdo %Inline;> <!-- I18N BiDi over-ride --> | |
660 | <!ATTLIST bdo | |
661 | %coreattrs; | |
662 | %events; | |
663 | lang %LanguageCode; #IMPLIED | |
664 | xml:lang %LanguageCode; #IMPLIED | |
665 | dir (ltr|rtl) #REQUIRED | |
666 | > | |
667 | ||
668 | <!ELEMENT br EMPTY> <!-- forced line break --> | |
669 | <!ATTLIST br | |
670 | %coreattrs; | |
671 | clear (left|all|right|none) "none" | |
672 | > | |
673 | ||
674 | <!ELEMENT em %Inline;> <!-- emphasis --> | |
675 | <!ATTLIST em %attrs;> | |
676 | ||
677 | <!ELEMENT strong %Inline;> <!-- strong emphasis --> | |
678 | <!ATTLIST strong %attrs;> | |
679 | ||
680 | <!ELEMENT dfn %Inline;> <!-- definitional --> | |
681 | <!ATTLIST dfn %attrs;> | |
682 | ||
683 | <!ELEMENT code %Inline;> <!-- program code --> | |
684 | <!ATTLIST code %attrs;> | |
685 | ||
686 | <!ELEMENT samp %Inline;> <!-- sample --> | |
687 | <!ATTLIST samp %attrs;> | |
688 | ||
689 | <!ELEMENT kbd %Inline;> <!-- something user would type --> | |
690 | <!ATTLIST kbd %attrs;> | |
691 | ||
692 | <!ELEMENT var %Inline;> <!-- variable --> | |
693 | <!ATTLIST var %attrs;> | |
694 | ||
695 | <!ELEMENT cite %Inline;> <!-- citation --> | |
696 | <!ATTLIST cite %attrs;> | |
697 | ||
698 | <!ELEMENT abbr %Inline;> <!-- abbreviation --> | |
699 | <!ATTLIST abbr %attrs;> | |
700 | ||
701 | <!ELEMENT acronym %Inline;> <!-- acronym --> | |
702 | <!ATTLIST acronym %attrs;> | |
703 | ||
704 | <!ELEMENT q %Inline;> <!-- inlined quote --> | |
705 | <!ATTLIST q | |
706 | %attrs; | |
707 | cite %URI; #IMPLIED | |
708 | > | |
709 | ||
710 | <!ELEMENT sub %Inline;> <!-- subscript --> | |
711 | <!ATTLIST sub %attrs;> | |
712 | ||
713 | <!ELEMENT sup %Inline;> <!-- superscript --> | |
714 | <!ATTLIST sup %attrs;> | |
715 | ||
716 | <!ELEMENT tt %Inline;> <!-- fixed pitch font --> | |
717 | <!ATTLIST tt %attrs;> | |
718 | ||
719 | <!ELEMENT i %Inline;> <!-- italic font --> | |
720 | <!ATTLIST i %attrs;> | |
721 | ||
722 | <!ELEMENT b %Inline;> <!-- bold font --> | |
723 | <!ATTLIST b %attrs;> | |
724 | ||
725 | <!ELEMENT big %Inline;> <!-- bigger font --> | |
726 | <!ATTLIST big %attrs;> | |
727 | ||
728 | <!ELEMENT small %Inline;> <!-- smaller font --> | |
729 | <!ATTLIST small %attrs;> | |
730 | ||
731 | <!ELEMENT u %Inline;> <!-- underline --> | |
732 | <!ATTLIST u %attrs;> | |
733 | ||
734 | <!ELEMENT s %Inline;> <!-- strike-through --> | |
735 | <!ATTLIST s %attrs;> | |
736 | ||
737 | <!ELEMENT strike %Inline;> <!-- strike-through --> | |
738 | <!ATTLIST strike %attrs;> | |
739 | ||
740 | <!ELEMENT basefont EMPTY> <!-- base font size --> | |
741 | <!ATTLIST basefont | |
742 | id ID #IMPLIED | |
743 | size CDATA #REQUIRED | |
744 | color %Color; #IMPLIED | |
745 | face CDATA #IMPLIED | |
746 | > | |
747 | ||
748 | <!ELEMENT font %Inline;> <!-- local change to font --> | |
749 | <!ATTLIST font | |
750 | %coreattrs; | |
751 | %i18n; | |
752 | size CDATA #IMPLIED | |
753 | color %Color; #IMPLIED | |
754 | face CDATA #IMPLIED | |
755 | > | |
756 | ||
757 | <!--==================== Object ======================================--> | |
758 | <!-- | |
759 | object is used to embed objects as part of HTML pages. | |
760 | param elements should precede other content. Parameters | |
761 | can also be expressed as attribute/value pairs on the | |
762 | object element itself when brevity is desired. | |
763 | --> | |
764 | ||
765 | <!ELEMENT object (#PCDATA | param | %block; | form | %inline; | %misc;)*> | |
766 | <!ATTLIST object | |
767 | %attrs; | |
768 | declare (declare) #IMPLIED | |
769 | classid %URI; #IMPLIED | |
770 | codebase %URI; #IMPLIED | |
771 | data %URI; #IMPLIED | |
772 | type %ContentType; #IMPLIED | |
773 | codetype %ContentType; #IMPLIED | |
774 | archive %UriList; #IMPLIED | |
775 | standby %Text; #IMPLIED | |
776 | height %Length; #IMPLIED | |
777 | width %Length; #IMPLIED | |
778 | usemap %URI; #IMPLIED | |
779 | name NMTOKEN #IMPLIED | |
780 | tabindex %Number; #IMPLIED | |
781 | align %ImgAlign; #IMPLIED | |
782 | border %Pixels; #IMPLIED | |
783 | hspace %Pixels; #IMPLIED | |
784 | vspace %Pixels; #IMPLIED | |
785 | > | |
786 | ||
787 | <!-- | |
788 | param is used to supply a named property value. | |
789 | In XML it would seem natural to follow RDF and support an | |
790 | abbreviated syntax where the param elements are replaced | |
791 | by attribute value pairs on the object start tag. | |
792 | --> | |
793 | <!ELEMENT param EMPTY> | |
794 | <!ATTLIST param | |
795 | id ID #IMPLIED | |
796 | name CDATA #REQUIRED | |
797 | value CDATA #IMPLIED | |
798 | valuetype (data|ref|object) "data" | |
799 | type %ContentType; #IMPLIED | |
800 | > | |
801 | ||
802 | <!--=================== Java applet ==================================--> | |
803 | <!-- | |
804 | One of code or object attributes must be present. | |
805 | Place param elements before other content. | |
806 | --> | |
807 | <!ELEMENT applet (#PCDATA | param | %block; | form | %inline; | %misc;)*> | |
808 | <!ATTLIST applet | |
809 | %coreattrs; | |
810 | codebase %URI; #IMPLIED | |
811 | archive CDATA #IMPLIED | |
812 | code CDATA #IMPLIED | |
813 | object CDATA #IMPLIED | |
814 | alt %Text; #IMPLIED | |
815 | name NMTOKEN #IMPLIED | |
816 | width %Length; #REQUIRED | |
817 | height %Length; #REQUIRED | |
818 | align %ImgAlign; #IMPLIED | |
819 | hspace %Pixels; #IMPLIED | |
820 | vspace %Pixels; #IMPLIED | |
821 | > | |
822 | ||
823 | <!--=================== Images ===========================================--> | |
824 | ||
825 | <!-- | |
826 | To avoid accessibility problems for people who aren't | |
827 | able to see the image, you should provide a text | |
828 | description using the alt and longdesc attributes. | |
829 | In addition, avoid the use of server-side image maps. | |
830 | --> | |
831 | ||
832 | <!ELEMENT img EMPTY> | |
833 | <!ATTLIST img | |
834 | %attrs; | |
835 | src %URI; #REQUIRED | |
836 | alt %Text; #REQUIRED | |
837 | name NMTOKEN #IMPLIED | |
838 | longdesc %URI; #IMPLIED | |
839 | height %Length; #IMPLIED | |
840 | width %Length; #IMPLIED | |
841 | usemap %URI; #IMPLIED | |
842 | ismap (ismap) #IMPLIED | |
843 | align %ImgAlign; #IMPLIED | |
844 | border %Length; #IMPLIED | |
845 | hspace %Pixels; #IMPLIED | |
846 | vspace %Pixels; #IMPLIED | |
847 | > | |
848 | ||
849 | <!-- usemap points to a map element which may be in this document | |
850 | or an external document, although the latter is not widely supported --> | |
851 | ||
852 | <!--================== Client-side image maps ============================--> | |
853 | ||
854 | <!-- These can be placed in the same document or grouped in a | |
855 | separate document although this isn't yet widely supported --> | |
856 | ||
857 | <!ELEMENT map ((%block; | form | %misc;)+ | area+)> | |
858 | <!ATTLIST map | |
859 | %i18n; | |
860 | %events; | |
861 | id ID #REQUIRED | |
862 | class CDATA #IMPLIED | |
863 | style %StyleSheet; #IMPLIED | |
864 | title %Text; #IMPLIED | |
865 | name CDATA #IMPLIED | |
866 | > | |
867 | ||
868 | <!ELEMENT area EMPTY> | |
869 | <!ATTLIST area | |
870 | %attrs; | |
871 | %focus; | |
872 | shape %Shape; "rect" | |
873 | coords %Coords; #IMPLIED | |
874 | href %URI; #IMPLIED | |
875 | nohref (nohref) #IMPLIED | |
876 | alt %Text; #REQUIRED | |
877 | target %FrameTarget; #IMPLIED | |
878 | > | |
879 | ||
880 | <!--================ Forms ===============================================--> | |
881 | ||
882 | <!ELEMENT form %form.content;> <!-- forms shouldn't be nested --> | |
883 | ||
884 | <!ATTLIST form | |
885 | %attrs; | |
886 | action %URI; #REQUIRED | |
887 | method (get|post) "get" | |
888 | name NMTOKEN #IMPLIED | |
889 | enctype %ContentType; "application/x-www-form-urlencoded" | |
890 | onsubmit %Script; #IMPLIED | |
891 | onreset %Script; #IMPLIED | |
892 | accept %ContentTypes; #IMPLIED | |
893 | accept-charset %Charsets; #IMPLIED | |
894 | target %FrameTarget; #IMPLIED | |
895 | > | |
896 | ||
897 | <!-- | |
898 | Each label must not contain more than ONE field | |
899 | Label elements shouldn't be nested. | |
900 | --> | |
901 | <!ELEMENT label %Inline;> | |
902 | <!ATTLIST label | |
903 | %attrs; | |
904 | for IDREF #IMPLIED | |
905 | accesskey %Character; #IMPLIED | |
906 | onfocus %Script; #IMPLIED | |
907 | onblur %Script; #IMPLIED | |
908 | > | |
909 | ||
910 | <!ENTITY % InputType | |
911 | "(text | password | checkbox | | |
912 | radio | submit | reset | | |
913 | file | hidden | image | button)" | |
914 | > | |
915 | ||
916 | <!-- the name attribute is required for all but submit & reset --> | |
917 | ||
918 | <!ELEMENT input EMPTY> <!-- form control --> | |
919 | <!ATTLIST input | |
920 | %attrs; | |
921 | %focus; | |
922 | type %InputType; "text" | |
923 | name CDATA #IMPLIED | |
924 | value CDATA #IMPLIED | |
925 | checked (checked) #IMPLIED | |
926 | disabled (disabled) #IMPLIED | |
927 | readonly (readonly) #IMPLIED | |
928 | size CDATA #IMPLIED | |
929 | maxlength %Number; #IMPLIED | |
930 | src %URI; #IMPLIED | |
931 | alt CDATA #IMPLIED | |
932 | usemap %URI; #IMPLIED | |
933 | onselect %Script; #IMPLIED | |
934 | onchange %Script; #IMPLIED | |
935 | accept %ContentTypes; #IMPLIED | |
936 | align %ImgAlign; #IMPLIED | |
937 | > | |
938 | ||
939 | <!ELEMENT select (optgroup|option)+> <!-- option selector --> | |
940 | <!ATTLIST select | |
941 | %attrs; | |
942 | name CDATA #IMPLIED | |
943 | size %Number; #IMPLIED | |
944 | multiple (multiple) #IMPLIED | |
945 | disabled (disabled) #IMPLIED | |
946 | tabindex %Number; #IMPLIED | |
947 | onfocus %Script; #IMPLIED | |
948 | onblur %Script; #IMPLIED | |
949 | onchange %Script; #IMPLIED | |
950 | > | |
951 | ||
952 | <!ELEMENT optgroup (option)+> <!-- option group --> | |
953 | <!ATTLIST optgroup | |
954 | %attrs; | |
955 | disabled (disabled) #IMPLIED | |
956 | label %Text; #REQUIRED | |
957 | > | |
958 | ||
959 | <!ELEMENT option (#PCDATA)> <!-- selectable choice --> | |
960 | <!ATTLIST option | |
961 | %attrs; | |
962 | selected (selected) #IMPLIED | |
963 | disabled (disabled) #IMPLIED | |
964 | label %Text; #IMPLIED | |
965 | value CDATA #IMPLIED | |
966 | > | |
967 | ||
968 | <!ELEMENT textarea (#PCDATA)> <!-- multi-line text field --> | |
969 | <!ATTLIST textarea | |
970 | %attrs; | |
971 | %focus; | |
972 | name CDATA #IMPLIED | |
973 | rows %Number; #REQUIRED | |
974 | cols %Number; #REQUIRED | |
975 | disabled (disabled) #IMPLIED | |
976 | readonly (readonly) #IMPLIED | |
977 | onselect %Script; #IMPLIED | |
978 | onchange %Script; #IMPLIED | |
979 | > | |
980 | ||
981 | <!-- | |
982 | The fieldset element is used to group form fields. | |
983 | Only one legend element should occur in the content | |
984 | and if present should only be preceded by whitespace. | |
985 | --> | |
986 | <!ELEMENT fieldset (#PCDATA | legend | %block; | form | %inline; | %misc;)*> | |
987 | <!ATTLIST fieldset | |
988 | %attrs; | |
989 | > | |
990 | ||
991 | <!ENTITY % LAlign "(top|bottom|left|right)"> | |
992 | ||
993 | <!ELEMENT legend %Inline;> <!-- fieldset label --> | |
994 | <!ATTLIST legend | |
995 | %attrs; | |
996 | accesskey %Character; #IMPLIED | |
997 | align %LAlign; #IMPLIED | |
998 | > | |
999 | ||
1000 | <!-- | |
1001 | Content is %Flow; excluding a, form, form controls, iframe | |
1002 | --> | |
1003 | <!ELEMENT button %button.content;> <!-- push button --> | |
1004 | <!ATTLIST button | |
1005 | %attrs; | |
1006 | %focus; | |
1007 | name CDATA #IMPLIED | |
1008 | value CDATA #IMPLIED | |
1009 | type (button|submit|reset) "submit" | |
1010 | disabled (disabled) #IMPLIED | |
1011 | > | |
1012 | ||
1013 | <!-- single-line text input control (DEPRECATED) --> | |
1014 | <!ELEMENT isindex EMPTY> | |
1015 | <!ATTLIST isindex | |
1016 | %coreattrs; | |
1017 | %i18n; | |
1018 | prompt %Text; #IMPLIED | |
1019 | > | |
1020 | ||
1021 | <!--======================= Tables =======================================--> | |
1022 | ||
1023 | <!-- Derived from IETF HTML table standard, see [RFC1942] --> | |
1024 | ||
1025 | <!-- | |
1026 | The border attribute sets the thickness of the frame around the | |
1027 | table. The default units are screen pixels. | |
1028 | ||
1029 | The frame attribute specifies which parts of the frame around | |
1030 | the table should be rendered. The values are not the same as | |
1031 | CALS to avoid a name clash with the valign attribute. | |
1032 | --> | |
1033 | <!ENTITY % TFrame "(void|above|below|hsides|lhs|rhs|vsides|box|border)"> | |
1034 | ||
1035 | <!-- | |
1036 | The rules attribute defines which rules to draw between cells: | |
1037 | ||
1038 | If rules is absent then assume: | |
1039 | "none" if border is absent or border="0" otherwise "all" | |
1040 | --> | |
1041 | ||
1042 | <!ENTITY % TRules "(none | groups | rows | cols | all)"> | |
1043 | ||
1044 | <!-- horizontal placement of table relative to document --> | |
1045 | <!ENTITY % TAlign "(left|center|right)"> | |
1046 | ||
1047 | <!-- horizontal alignment attributes for cell contents | |
1048 | ||
1049 | char alignment char, e.g. char=':' | |
1050 | charoff offset for alignment char | |
1051 | --> | |
1052 | <!ENTITY % cellhalign | |
1053 | "align (left|center|right|justify|char) #IMPLIED | |
1054 | char %Character; #IMPLIED | |
1055 | charoff %Length; #IMPLIED" | |
1056 | > | |
1057 | ||
1058 | <!-- vertical alignment attributes for cell contents --> | |
1059 | <!ENTITY % cellvalign | |
1060 | "valign (top|middle|bottom|baseline) #IMPLIED" | |
1061 | > | |
1062 | ||
1063 | <!ELEMENT table | |
1064 | (caption?, (col*|colgroup*), thead?, tfoot?, (tbody+|tr+))> | |
1065 | <!ELEMENT caption %Inline;> | |
1066 | <!ELEMENT thead (tr)+> | |
1067 | <!ELEMENT tfoot (tr)+> | |
1068 | <!ELEMENT tbody (tr)+> | |
1069 | <!ELEMENT colgroup (col)*> | |
1070 | <!ELEMENT col EMPTY> | |
1071 | <!ELEMENT tr (th|td)+> | |
1072 | <!ELEMENT th %Flow;> | |
1073 | <!ELEMENT td %Flow;> | |
1074 | ||
1075 | <!ATTLIST table | |
1076 | %attrs; | |
1077 | summary %Text; #IMPLIED | |
1078 | width %Length; #IMPLIED | |
1079 | border %Pixels; #IMPLIED | |
1080 | frame %TFrame; #IMPLIED | |
1081 | rules %TRules; #IMPLIED | |
1082 | cellspacing %Length; #IMPLIED | |
1083 | cellpadding %Length; #IMPLIED | |
1084 | align %TAlign; #IMPLIED | |
1085 | bgcolor %Color; #IMPLIED | |
1086 | > | |
1087 | ||
1088 | <!ENTITY % CAlign "(top|bottom|left|right)"> | |
1089 | ||
1090 | <!ATTLIST caption | |
1091 | %attrs; | |
1092 | align %CAlign; #IMPLIED | |
1093 | > | |
1094 | ||
1095 | <!-- | |
1096 | colgroup groups a set of col elements. It allows you to group | |
1097 | several semantically related columns together. | |
1098 | --> | |
1099 | <!ATTLIST colgroup | |
1100 | %attrs; | |
1101 | span %Number; "1" | |
1102 | width %MultiLength; #IMPLIED | |
1103 | %cellhalign; | |
1104 | %cellvalign; | |
1105 | > | |
1106 | ||
1107 | <!-- | |
1108 | col elements define the alignment properties for cells in | |
1109 | one or more columns. | |
1110 | ||
1111 | The width attribute specifies the width of the columns, e.g. | |
1112 | ||
1113 | width=64 width in screen pixels | |
1114 | width=0.5* relative width of 0.5 | |
1115 | ||
1116 | The span attribute causes the attributes of one | |
1117 | col element to apply to more than one column. | |
1118 | --> | |
1119 | <!ATTLIST col | |
1120 | %attrs; | |
1121 | span %Number; "1" | |
1122 | width %MultiLength; #IMPLIED | |
1123 | %cellhalign; | |
1124 | %cellvalign; | |
1125 | > | |
1126 | ||
1127 | <!-- | |
1128 | Use thead to duplicate headers when breaking table | |
1129 | across page boundaries, or for static headers when | |
1130 | tbody sections are rendered in scrolling panel. | |
1131 | ||
1132 | Use tfoot to duplicate footers when breaking table | |
1133 | across page boundaries, or for static footers when | |
1134 | tbody sections are rendered in scrolling panel. | |
1135 | ||
1136 | Use multiple tbody sections when rules are needed | |
1137 | between groups of table rows. | |
1138 | --> | |
1139 | <!ATTLIST thead | |
1140 | %attrs; | |
1141 | %cellhalign; | |
1142 | %cellvalign; | |
1143 | > | |
1144 | ||
1145 | <!ATTLIST tfoot | |
1146 | %attrs; | |
1147 | %cellhalign; | |
1148 | %cellvalign; | |
1149 | > | |
1150 | ||
1151 | <!ATTLIST tbody | |
1152 | %attrs; | |
1153 | %cellhalign; | |
1154 | %cellvalign; | |
1155 | > | |
1156 | ||
1157 | <!ATTLIST tr | |
1158 | %attrs; | |
1159 | %cellhalign; | |
1160 | %cellvalign; | |
1161 | bgcolor %Color; #IMPLIED | |
1162 | > | |
1163 | ||
1164 | <!-- Scope is simpler than headers attribute for common tables --> | |
1165 | <!ENTITY % Scope "(row|col|rowgroup|colgroup)"> | |
1166 | ||
1167 | <!-- th is for headers, td for data and for cells acting as both --> | |
1168 | ||
1169 | <!ATTLIST th | |
1170 | %attrs; | |
1171 | abbr %Text; #IMPLIED | |
1172 | axis CDATA #IMPLIED | |
1173 | headers IDREFS #IMPLIED | |
1174 | scope %Scope; #IMPLIED | |
1175 | rowspan %Number; "1" | |
1176 | colspan %Number; "1" | |
1177 | %cellhalign; | |
1178 | %cellvalign; | |
1179 | nowrap (nowrap) #IMPLIED | |
1180 | bgcolor %Color; #IMPLIED | |
1181 | width %Length; #IMPLIED | |
1182 | height %Length; #IMPLIED | |
1183 | > | |
1184 | ||
1185 | <!ATTLIST td | |
1186 | %attrs; | |
1187 | abbr %Text; #IMPLIED | |
1188 | axis CDATA #IMPLIED | |
1189 | headers IDREFS #IMPLIED | |
1190 | scope %Scope; #IMPLIED | |
1191 | rowspan %Number; "1" | |
1192 | colspan %Number; "1" | |
1193 | %cellhalign; | |
1194 | %cellvalign; | |
1195 | nowrap (nowrap) #IMPLIED | |
1196 | bgcolor %Color; #IMPLIED | |
1197 | width %Length; #IMPLIED | |
1198 | height %Length; #IMPLIED | |
1199 | > | |
1200 |
0 | ID 100K_RAT STANDARD; PRT; 889 AA. | |
1 | AC Q62671; | |
2 | DT 01-NOV-1997 (Rel. 35, Created) | |
3 | DT 01-NOV-1997 (Rel. 35, Last sequence update) | |
4 | DT 15-JUL-1999 (Rel. 38, Last annotation update) | |
5 | DE 100 KD PROTEIN (EC 6.3.2.-). | |
6 | OS Rattus norvegicus (Rat). | |
7 | OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Mammalia; | |
8 | OC Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Rattus. | |
9 | RN [1] | |
10 | RP SEQUENCE FROM N.A. | |
11 | RC STRAIN=WISTAR; TISSUE=TESTIS; | |
12 | RX MEDLINE; 92253337. | |
13 | RA MUELLER D., REHBEIN M., BAUMEISTER H., RICHTER D.; | |
14 | RT "Molecular characterization of a novel rat protein structurally | |
15 | RT related to poly(A) binding proteins and the 70K protein of the U1 | |
16 | RT small nuclear ribonucleoprotein particle (snRNP)."; | |
17 | RL Nucleic Acids Res. 20:1471-1475(1992). | |
18 | RN [2] | |
19 | RP ERRATUM. | |
20 | RA MUELLER D., REHBEIN M., BAUMEISTER H., RICHTER D.; | |
21 | RL Nucleic Acids Res. 20:2624-2624(1992). | |
22 | CC -!- FUNCTION: E3 UBIQUITIN-PROTEIN LIGASE WHICH ACCEPTS UBIQUITIN FROM | |
23 | CC AN E2 UBIQUITIN-CONJUGATING ENZYME IN THE FORM OF A THIOESTER AND | |
24 | CC THEN DIRECTLY TRANSFERS THE UBIQUITIN TO TARGETED SUBSTRATES (BY | |
25 | CC SIMILARITY). THIS PROTEIN MAY BE INVOLVED IN MATURATION AND/OR | |
26 | CC POST-TRANSCRIPTIONAL REGULATION OF MRNA. | |
27 | CC -!- TISSUE SPECIFICITY: HIGHEST LEVELS FOUND IN TESTIS. ALSO PRESENT | |
28 | CC IN LIVER, KIDNEY, LUNG AND BRAIN. | |
29 | CC -!- DEVELOPMENTAL STAGE: IN EARLY POST-NATAL LIFE, EXPRESSION IN | |
30 | CC THE TESTIS INCREASES TO REACH A MAXIMUM AROUND DAY 28. | |
31 | CC -!- MISCELLANEOUS: A CYSTEINE RESIDUE IS REQUIRED FOR | |
32 | CC UBIQUITIN-THIOLESTER FORMATION. | |
33 | CC -!- SIMILARITY: CONTAINS AN HECT-TYPE E3 UBIQUITIN-PROTEIN LIGASE | |
34 | CC DOMAIN. | |
35 | CC -!- SIMILARITY: A CENTRAL REGION (AA 485-514) IS SIMILAR TO THE | |
36 | CC C-TERMINAL DOMAINS OF MAMMALIAN AND YEAST POLY (A) RNA BINDING | |
37 | CC PROTEINS (PABP). | |
38 | CC -!- SIMILARITY: THE C-TERMINAL HALF SHOWS HIGH SIMILARITY TO | |
39 | CC DROSOPHILA HYPERPLASMIC DISC PROTEIN AND SOME, TO HUMAN E6-AP. | |
40 | CC -!- SIMILARITY: CONTAINS MIXED-CHARGE DOMAINS SIMILAR TO RNA-BINDING | |
41 | CC PROTEINS. | |
42 | CC -------------------------------------------------------------------------- | |
43 | CC This SWISS-PROT entry is copyright. It is produced through a collaboration | |
44 | CC between the Swiss Institute of Bioinformatics and the EMBL outstation - | |
45 | CC the European Bioinformatics Institute. There are no restrictions on its | |
46 | CC use by non-profit institutions as long as its content is in no way | |
47 | CC modified and this statement is not removed. Usage by and for commercial | |
48 | CC entities requires a license agreement (See http://www.isb-sib.ch/announce/ | |
49 | CC or send an email to license@isb-sib.ch). | |
50 | CC -------------------------------------------------------------------------- | |
51 | DR EMBL; X64411; CAA45756.1; -. | |
52 | DR PFAM; PF00632; HECT; 1. | |
53 | DR PFAM; PF00658; PABP; 1. | |
54 | KW Ubiquitin conjugation; Ligase. | |
55 | FT DOMAIN 77 88 ASP/GLU-RICH (ACIDIC). | |
56 | FT DOMAIN 127 150 PRO-RICH. | |
57 | FT DOMAIN 420 439 ARG/GLU-RICH (MIXED CHARGE). | |
58 | FT DOMAIN 448 457 ARG/ASP-RICH (MIXED CHARGE). | |
59 | FT DOMAIN 485 514 PABP-LIKE. | |
60 | FT DOMAIN 579 590 ASP/GLU-RICH (ACIDIC). | |
61 | FT DOMAIN 786 889 HECT DOMAIN. | |
62 | FT DOMAIN 827 847 PRO-RICH. | |
63 | FT BINDING 858 858 UBIQUITIN (BY SIMILARITY). | |
64 | SQ SEQUENCE 889 AA; 100368 MW; DD7E6C7A CRC32; | |
65 | MMSARGDFLN YALSLMRSHN DEHSDVLPVL DVCSLKHVAY VFQALIYWIK AMNQQTTLDT | |
66 | PQLERKRTRE LLELGIDNED SEHENDDDTS QSATLNDKDD ESLPAETGQN HPFFRRSDSM | |
67 | TFLGCIPPNP FEVPLAEAIP LADQPHLLQP NARKEDLFGR PSQGLYSSSA GSGKCLVEVT | |
68 | MDRNCLEVLP TKMSYAANLK NVMNMQNRQK KAGEDQSMLA EEADSSKPGP SAHDVAAQLK | |
69 | SSLLAEIGLT ESEGPPLTSF RPQCSFMGMV ISHDMLLGRW RLSLELFGRV FMEDVGAEPG | |
70 | SILTELGGFE VKESKFRREM EKLRNQQSRD LSLEVDRDRD LLIQQTMRQL NNHFGRRCAT | |
71 | TPMAVHRVKV TFKDEPGEGS GVARSFYTAI AQAFLSNEKL PNLDCIQNAN KGTHTSLMQR | |
72 | LRNRGERDRE REREREMRRS SGLRAGSRRD RDRDFRRQLS IDTRPFRPAS EGNPSDDPDP | |
73 | LPAHRQALGE RLYPRVQAMQ PAFASKITGM LLELSPAQLL LLLASEDSLR ARVEEAMELI | |
74 | VAHGRENGAD SILDLGLLDS SEKVQENRKR HGSSRSVVDM DLDDTDDGDD NAPLFYQPGK | |
75 | RGFYTPRPGK NTEARLNCFR NIGRILGLCL LQNELCPITL NRHVIKVLLG RKVNWHDFAF | |
76 | FDPVMYESLR QLILASQSSD ADAVFSAMDL AFAVDLCKEE GGGQVELIPN GVNIPVTPQN | |
77 | VYEYVRKYAE HRMLVVAEQP LHAMRKGLLD VLPKNSLEDL TAEDFRLLVN GCGEVNVQML | |
78 | ISFTSFNDES GENAEKLLQF KRWFWSIVER MSMTERQDLV YFWTSSPSLP ASEEGFQPMP | |
79 | SITIRPPDDQ HLPTANTCIS RLYVPLYSSK QILKQKLLLA IKTKNFGFV | |
80 | // | |
81 | ID 104K_THEPA STANDARD; PRT; 924 AA. | |
82 | AC P15711; | |
83 | DT 01-APR-1990 (Rel. 14, Created) | |
84 | DT 01-APR-1990 (Rel. 14, Last sequence update) | |
85 | DT 01-AUG-1992 (Rel. 23, Last annotation update) | |
86 | DE 104 KD MICRONEME-RHOPTRY ANTIGEN. | |
87 | OS Theileria parva. | |
88 | OC Eukaryota; Alveolata; Apicomplexa; Piroplasmida; Theileriidae; | |
89 | OC Theileria. | |
90 | RN [1] | |
91 | RP SEQUENCE FROM N.A. | |
92 | RC STRAIN=MUGUGA; | |
93 | RX MEDLINE; 90158697. | |
94 | RA IAMS K.P., YOUNG J.R., NENE V., DESAI J., WEBSTER P., | |
95 | RA OLE-MOIYOI O.K., MUSOKE A.J.; | |
96 | RT "Characterisation of the gene encoding a 104-kilodalton microneme- | |
97 | RT rhoptry protein of Theileria parva."; | |
98 | RL Mol. Biochem. Parasitol. 39:47-60(1990). | |
99 | CC -!- SUBCELLULAR LOCATION: IN MICRONEME/RHOPTRY COMPLEXES. | |
100 | CC -!- DEVELOPMENTAL STAGE: SPOROZOITE ANTIGEN. | |
101 | CC -------------------------------------------------------------------------- | |
102 | CC This SWISS-PROT entry is copyright. It is produced through a collaboration | |
103 | CC between the Swiss Institute of Bioinformatics and the EMBL outstation - | |
104 | CC the European Bioinformatics Institute. There are no restrictions on its | |
105 | CC use by non-profit institutions as long as its content is in no way | |
106 | CC modified and this statement is not removed. Usage by and for commercial | |
107 | CC entities requires a license agreement (See http://www.isb-sib.ch/announce/ | |
108 | CC or send an email to license@isb-sib.ch). | |
109 | CC -------------------------------------------------------------------------- | |
110 | DR EMBL; M29954; AAA18217.1; -. | |
111 | DR PIR; A44945; A44945. | |
112 | KW Antigen; Sporozoite; Repeat. | |
113 | FT DOMAIN 1 19 HYDROPHOBIC. | |
114 | FT DOMAIN 905 924 HYDROPHOBIC. | |
115 | SQ SEQUENCE 924 AA; 103625 MW; 4563AAA0 CRC32; | |
116 | MKFLILLFNI LCLFPVLAAD NHGVGPQGAS GVDPITFDIN SNQTGPAFLT AVEMAGVKYL | |
117 | QVQHGSNVNI HRLVEGNVVI WENASTPLYT GAIVTNNDGP YMAYVEVLGD PNLQFFIKSG | |
118 | DAWVTLSEHE YLAKLQEIRQ AVHIESVFSL NMAFQLENNK YEVETHAKNG ANMVTFIPRN | |
119 | GHICKMVYHK NVRIYKATGN DTVTSVVGFF RGLRLLLINV FSIDDNGMMS NRYFQHVDDK | |
120 | YVPISQKNYE TGIVKLKDYK HAYHPVDLDI KDIDYTMFHL ADATYHEPCF KIIPNTGFCI | |
121 | TKLFDGDQVL YESFNPLIHC INEVHIYDRN NGSIICLHLN YSPPSYKAYL VLKDTGWEAT | |
122 | THPLLEEKIE ELQDQRACEL DVNFISDKDL YVAALTNADL NYTMVTPRPH RDVIRVSDGS | |
123 | EVLWYYEGLD NFLVCAWIYV SDGVASLVHL RIKDRIPANN DIYVLKGDLY WTRITKIQFT | |
124 | QEIKRLVKKS KKKLAPITEE DSDKHDEPPE GPGASGLPPK APGDKEGSEG HKGPSKGSDS | |
125 | SKEGKKPGSG KKPGPAREHK PSKIPTLSKK PSGPKDPKHP RDPKEPRKSK SPRTASPTRR | |
126 | PSPKLPQLSK LPKSTSPRSP PPPTRPSSPE RPEGTKIIKT SKPPSPKPPF DPSFKEKFYD | |
127 | DYSKAASRSK ETKTTVVLDE SFESILKETL PETPGTPFTT PRPVPPKRPR TPESPFEPPK | |
128 | DPDSPSTSPS EFFTPPESKR TRFHETPADT PLPDVTAELF KEPDVTAETK SPDEAMKRPR | |
129 | SPSEYEDTSP GDYPSLPMKR HRLERLRLTT TEMETDPGRM AKDASGKPVK LKRSKSFDDL | |
130 | TTVELAPEPK ASRIVVDDEG TEADDEETHP PEERQKTEVR RRRPPKKPSK SPRPSKPKKP | |
131 | KKPDSAYIPS ILAILVVSLI VGIL | |
132 | // | |
133 | ID 108_LYCES STANDARD; PRT; 102 AA. | |
134 | AC Q43495; | |
135 | DT 15-JUL-1999 (Rel. 38, Created) | |
136 | DT 15-JUL-1999 (Rel. 38, Last sequence update) | |
137 | DT 15-JUL-1999 (Rel. 38, Last annotation update) | |
138 | DE PROTEIN 108 PRECURSOR. | |
139 | OS Lycopersicon esculentum (Tomato). | |
140 | OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; | |
141 | OC euphyllophytes; Spermatophyta; Magnoliophyta; eudicotyledons; | |
142 | OC core eudicots; Asteridae; euasterids I; Solanales; Solanaceae; | |
143 | OC Solanum. | |
144 | RN [1] | |
145 | RP SEQUENCE FROM N.A. | |
146 | RC STRAIN=CV. VF36; TISSUE=ANTHER; | |
147 | RX MEDLINE; 94143497. | |
148 | RA CHEN R., SMITH A.G.; | |
149 | RT "Nucleotide sequence of a stamen- and tapetum-specific gene from | |
150 | RT Lycopersicon esculentum."; | |
151 | RL Plant Physiol. 101:1413-1413(1993). | |
152 | CC -!- TISSUE SPECIFICITY: STAMEN- AND TAPETUM-SPECIFIC. | |
153 | CC -!- SIMILARITY: BELONGS TO THE A9 / FIL1 FAMILY. | |
154 | CC -------------------------------------------------------------------------- | |
155 | CC This SWISS-PROT entry is copyright. It is produced through a collaboration | |
156 | CC between the Swiss Institute of Bioinformatics and the EMBL outstation - | |
157 | CC the European Bioinformatics Institute. There are no restrictions on its | |
158 | CC use by non-profit institutions as long as its content is in no way | |
159 | CC modified and this statement is not removed. Usage by and for commercial | |
160 | CC entities requires a license agreement (See http://www.isb-sib.ch/announce/ | |
161 | CC or send an email to license@isb-sib.ch). | |
162 | CC -------------------------------------------------------------------------- | |
163 | DR EMBL; Z14088; CAA78466.1; -. | |
164 | DR MENDEL; 8853; LYCes;1133;1. | |
165 | KW Signal. | |
166 | FT SIGNAL 1 30 POTENTIAL. | |
167 | FT CHAIN 31 102 PROTEIN 108. | |
168 | FT DISULFID 41 77 BY SIMILARITY. | |
169 | FT DISULFID 51 66 BY SIMILARITY. | |
170 | FT DISULFID 67 92 BY SIMILARITY. | |
171 | FT DISULFID 79 99 BY SIMILARITY. | |
172 | SQ SEQUENCE 102 AA; 10576 MW; AFA4875A CRC32; | |
173 | MASVKSSSSS SSSSFISLLL LILLVIVLQS QVIECQPQQS CTASLTGLNV CAPFLVPGSP | |
174 | TASTECCNAV QSINHDCMCN TMRIAAQIPA QCNLPPLSCS AN | |
175 | // |