diff --git a/debian/control b/debian/control index 95de184..840bcb9 100644 --- a/debian/control +++ b/debian/control @@ -5,7 +5,7 @@ DM-Upload-Allowed: yes Uploaders: Steffen Moeller , Andreas Tille -Build-Depends: debhelper (>= 5.0), docbook-to-man, gzip, cdbs, quilt +Build-Depends: debhelper (>= 5.0), docbook-to-man, cdbs, quilt Standards-Version: 3.7.3 Homepage: http://www.tigr.org/software/glimmer/ Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/tigr-glimmer/trunk/?rev=0&sc=0 diff --git a/debian/long-orfs.1 b/debian/long-orfs.1 index b8639b0..bc57925 100644 --- a/debian/long-orfs.1 +++ b/debian/long-orfs.1 @@ -49,142 +49,142 @@ .ds f2\" .ds f3\" .ds f4\" -'\" t -.ta 8n 16n 24n 32n 40n 48n 56n 64n 72n -.TH "LONG-ORFS" "1" -.SH "NAME" -long-orfs \(em Find/Score potential genes in genome-file using -the probability model in icm-file -.SH "SYNOPSIS" -.PP -\fBlong-orgs\fR [genome-file \fB\fIoptions\fR\fP] -.SH "DESCRIPTION" -.PP -Program long-orfs takes a sequence file (in FASTA format) and -outputs a list of all long "potential genes" in it that do not -overlap by too much. By "potential gene" I mean the portion of -an orf from the first start codon to the stop codon at the end. -.PP -The first few lines of output specify the settings of various -parameters in the program: -.PP -Minimum gene length is the length of the smallest fragment -considered to be a gene. The length is measured from the first base -of the start codon to the last base *before* the stop codon. -This value can be specified when running the program with the -g option. -By default, the program now (April 2003) will compute an optimal length -for this parameter, where "optimal" is the value that produces the -greatest number of long ORFs, thereby increasing the amount of data -used for training. -.PP -Minimum overlap length is a lower bound on the number of bases overlap -between 2 genes that is considered a problem. Overlaps shorter than -this are ignored. -.PP -Minimum overlap percent is another lower bound on the number of bases -overlap that is considered a problem. Overlaps shorter than this -percentage of *both* genes are ignored. -.PP -The next portion of the output is a list of potential genes: -.PP -Column 1 is an ID number for reference purposes. It is assigned -sequentially starting with 1 to all long potential genes. If -overlapping genes are eliminated, gaps in the numbers will occur. -The ID prefix is specified in the constant ID_PREFIX . -.PP -Column 2 is the position of the first base of the first start codon in -the orf. Currently I use atg, and gtg as start codons. This is -easily changed in the function Is_Start () . -.PP -Column 3 is the position of the last base *before* the stop codon. Stop -codons are taa, tag, and tga. Note that for orfs in the reverse -reading frames have their start position higher than the end position. -The order in which orfs are listed is in increasing order by -Max {OrfStart, End}, i.e., the highest numbered position in the orf, -except for orfs that "wrap around" the end of the sequence. -.PP -When two genes with ID numbers overlap by at least a sufficient -amount (as determined by Min_Olap and Min_Olap_Percent ), they -are eliminated and do not appear in the output. -.PP -The final output of the program (sent to the standard error file so -it does not show up when output is redirected to a file) is the -length of the longest orf found. -.PP - -Specifying Different Start and Stop Codons: -.PP -To specify different sets of start and stop codons, modify the file -gene.h . Specifically, the functions: -.PP -Is_Forward_Start Is_Reverse_Start Is_Start -Is_Forward_Stop Is_Reverse_Stop Is_Stop -.PP -are used to determine what is used for start and stop codons. -.PP -Is_Start and Is_Stop do simple string comparisons to specify -which patterns are used. To add a new pattern, just add the comparison -for it. To remove a pattern, comment out or delete the comparison -for it. -.PP -The other four functions use a bit comparison to determine start and -stop patterns. They represent a codon as a 12-bit pattern, with 4 bits -for each base, one bit for each possible value of the bases, T, G, C -or A. Thus the bit pattern 0010 0101 1100 represents the base -pattern [C] [A or G] [G or T]. By doing bit operations (& | ~) and -comparisons, more complicated patterns involving ambiguous reads -can be tested efficiently. Simple patterns can be tested as in -the current code. -.PP -For example, to insert an additional start codon of CAT requires 3 changes: -1. The line -|| (Codon & 0x218) == Codon -should be inserted into Is_Forward_Start , since 0x218 = 0010 0001 1000 -represents CAT. -2. The line -|| (Codon & 0x184) == Codon -should be inserted into Is_Reverse_Start , since 0x184 = 0001 1000 0100 -represents ATG, which is the reverse-complement of CAT. Alternately, -the #define constant ATG_MASK could be used. -3. The line -|| strncmp (S, "cat", 3) == 0 -should be inserted into Is_Start . -.SH "OPTIONS" -.IP "\fB-g \fIn\fR\fP" 10 -Set minimum gene length to n. Default is to compute an -optimal value automatically. Don't change this unless you -know what you're doing. -.IP "\fB-l\fP" 10 -Regard the genome as linear (not circular), i.e., do not allow -genes to "wrap around" the end of the genome. -This option works on both glimmer and long-orfs . -The default behavior is to regard the genome as circular. -.IP "\fB-o \fIn\fR\fP" 10 -Set maximum overlap length to n. Overlaps shorter than this -are permitted. (Default is 0 bp.) -.IP "\fB-p \fIn\fR\fP" 10 -Set maximum overlap percentage to n%. Overlaps shorter than -this percentage of *both* strings are ignored. (Default is 10%.) -.SH "SEE ALSO" -.PP -glimmer2 (1), -adjust (1), -anomaly (1), -build-icm (1), -check (1), -codon-usage (1), -compare-lists (1), -extract (1), -generate (1), -get-len (1), -get-putative (1), -.PP -http://www.tigr.org/software/glimmer/ -.PP -Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer2. -.SH "AUTHOR" -.PP -This manual page was quickly copied from the glimmer web site by Steffen Moeller moeller@pzr.uni-rostock.de for -the \fBDebian\fP system. - -...\" created by instant / docbook-to-man, Sun 09 Nov 2003, 19:43 +'\" t +.ta 8n 16n 24n 32n 40n 48n 56n 64n 72n +.TH "LONG-ORFS" "1" +.SH "NAME" +long-orfs \(em Find/Score potential genes in genome-file using +the probability model in icm-file +.SH "SYNOPSIS" +.PP +\fBlong-orgs\fR [genome-file \fB\fIoptions\fR\fP] +.SH "DESCRIPTION" +.PP +Program long-orfs takes a sequence file (in FASTA format) and +outputs a list of all long "potential genes" in it that do not +overlap by too much. By "potential gene" I mean the portion of +an orf from the first start codon to the stop codon at the end. +.PP +The first few lines of output specify the settings of various +parameters in the program: +.PP +Minimum gene length is the length of the smallest fragment +considered to be a gene. The length is measured from the first base +of the start codon to the last base *before* the stop codon. +This value can be specified when running the program with the -g option. +By default, the program now (April 2003) will compute an optimal length +for this parameter, where "optimal" is the value that produces the +greatest number of long ORFs, thereby increasing the amount of data +used for training. +.PP +Minimum overlap length is a lower bound on the number of bases overlap +between 2 genes that is considered a problem. Overlaps shorter than +this are ignored. +.PP +Minimum overlap percent is another lower bound on the number of bases +overlap that is considered a problem. Overlaps shorter than this +percentage of *both* genes are ignored. +.PP +The next portion of the output is a list of potential genes: +.PP +Column 1 is an ID number for reference purposes. It is assigned +sequentially starting with 1 to all long potential genes. If +overlapping genes are eliminated, gaps in the numbers will occur. +The ID prefix is specified in the constant ID_PREFIX . +.PP +Column 2 is the position of the first base of the first start codon in +the orf. Currently I use atg, and gtg as start codons. This is +easily changed in the function Is_Start () . +.PP +Column 3 is the position of the last base *before* the stop codon. Stop +codons are taa, tag, and tga. Note that for orfs in the reverse +reading frames have their start position higher than the end position. +The order in which orfs are listed is in increasing order by +Max {OrfStart, End}, i.e., the highest numbered position in the orf, +except for orfs that "wrap around" the end of the sequence. +.PP +When two genes with ID numbers overlap by at least a sufficient +amount (as determined by Min_Olap and Min_Olap_Percent ), they +are eliminated and do not appear in the output. +.PP +The final output of the program (sent to the standard error file so +it does not show up when output is redirected to a file) is the +length of the longest orf found. +.PP + +Specifying Different Start and Stop Codons: +.PP +To specify different sets of start and stop codons, modify the file +gene.h . Specifically, the functions: +.PP +Is_Forward_Start Is_Reverse_Start Is_Start +Is_Forward_Stop Is_Reverse_Stop Is_Stop +.PP +are used to determine what is used for start and stop codons. +.PP +Is_Start and Is_Stop do simple string comparisons to specify +which patterns are used. To add a new pattern, just add the comparison +for it. To remove a pattern, comment out or delete the comparison +for it. +.PP +The other four functions use a bit comparison to determine start and +stop patterns. They represent a codon as a 12-bit pattern, with 4 bits +for each base, one bit for each possible value of the bases, T, G, C +or A. Thus the bit pattern 0010 0101 1100 represents the base +pattern [C] [A or G] [G or T]. By doing bit operations (& | ~) and +comparisons, more complicated patterns involving ambiguous reads +can be tested efficiently. Simple patterns can be tested as in +the current code. +.PP +For example, to insert an additional start codon of CAT requires 3 changes: +1. The line +|| (Codon & 0x218) == Codon +should be inserted into Is_Forward_Start , since 0x218 = 0010 0001 1000 +represents CAT. +2. The line +|| (Codon & 0x184) == Codon +should be inserted into Is_Reverse_Start , since 0x184 = 0001 1000 0100 +represents ATG, which is the reverse-complement of CAT. Alternately, +the #define constant ATG_MASK could be used. +3. The line +|| strncmp (S, "cat", 3) == 0 +should be inserted into Is_Start . +.SH "OPTIONS" +.IP "\fB-g \fIn\fR\fP" 10 +Set minimum gene length to n. Default is to compute an +optimal value automatically. Don't change this unless you +know what you're doing. +.IP "\fB-l\fP" 10 +Regard the genome as linear (not circular), i.e., do not allow +genes to "wrap around" the end of the genome. +This option works on both glimmer and long-orfs . +The default behavior is to regard the genome as circular. +.IP "\fB-o \fIn\fR\fP" 10 +Set maximum overlap length to n. Overlaps shorter than this +are permitted. (Default is 0 bp.) +.IP "\fB-p \fIn\fR\fP" 10 +Set maximum overlap percentage to n%. Overlaps shorter than +this percentage of *both* strings are ignored. (Default is 10%.) +.SH "SEE ALSO" +.PP +glimmer3 (1), +adjust (1), +anomaly (1), +build-icm (1), +check (1), +codon-usage (1), +compare-lists (1), +extract (1), +generate (1), +get-len (1), +get-putative (1), +.PP +http://www.tigr.org/software/glimmer/ +.PP +Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer3. +.SH "AUTHOR" +.PP +This manual page was quickly copied from the glimmer web site by Steffen Moeller moeller@pzr.uni-rostock.de for +the \fBDebian\fP system. + +...\" created by instant / docbook-to-man, Sun 09 Nov 2003, 19:43 diff --git a/debian/manpages b/debian/manpages index bd4d49d..e26562c 100644 --- a/debian/manpages +++ b/debian/manpages @@ -1,13 +1 @@ -debian/tigr-adjust.1 -debian/tigr-anomaly.1 -debian/tigr-build-icm.1 -debian/tigr-check.1 -debian/tigr-codon-usage.1 -debian/tigr-compare-lists.1 -debian/tigr-extract.1 -debian/tigr-generate.1 -debian/tigr-get-len.1 -debian/tigr-get-putative.1 -debian/tigr-glimmer2.1 -debian/tigr-long-orfs.1 -debian/tigr-run-glimmer2.1 +debian/tigr-*.1 diff --git a/debian/rules b/debian/rules index 0d4fdca..543f48f 100755 --- a/debian/rules +++ b/debian/rules @@ -6,7 +6,7 @@ include /usr/share/cdbs/1/rules/debhelper.mk include /usr/share/cdbs/1/class/makefile.mk -MANPAGES=debian/tigr-adjust.1 debian/tigr-anomaly.1 debian/tigr-build-icm.1 debian/tigr-check.1 debian/tigr-codon-usage.1 debian/tigr-compare-lists.1 debian/tigr-extract.1 debian/tigr-generate.1 debian/tigr-get-len.1 debian/tigr-get-putative.1 debian/tigr-run-glimmer2.1 debian/tigr-glimmer2.1 debian/tigr-long-orfs.1 +MANPAGES=debian/tigr-adjust.1 debian/tigr-anomaly.1 debian/tigr-build-icm.1 debian/tigr-check.1 debian/tigr-codon-usage.1 debian/tigr-compare-lists.1 debian/tigr-extract.1 debian/tigr-generate.1 debian/tigr-get-len.1 debian/tigr-get-putative.1 debian/tigr-run-glimmer3.1 debian/tigr-glimmer3.1 debian/tigr-long-orfs.1 .SUFFIXES: .1 .sgml @@ -14,7 +14,7 @@ docbook-to-man $< > $@ clean:: - dh_clean $(MANPAGES) tigr-run-glimmer2 + dh_clean $(MANPAGES) rm -f bin/* lib/* obj/* build/tigr-glimmer:: $(MANPAGES) diff --git a/debian/tigr-adjust.sgml b/debian/tigr-adjust.sgml index dfc2f86..8d11ab6 100644 --- a/debian/tigr-adjust.sgml +++ b/debian/tigr-adjust.sgml @@ -72,7 +72,7 @@ SEE ALSO -tigr-glimmer2 (1), +tigr-glimmer3 (1), tigr-adjust (1), tigr-anomaly (1), tigr-build-icm (1), @@ -89,7 +89,7 @@ http://www.tigr.org/software/glimmer/ - Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer2. + Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer3. AUTHOR diff --git a/debian/tigr-anomaly.sgml b/debian/tigr-anomaly.sgml index ba30663..925f844 100644 --- a/debian/tigr-anomaly.sgml +++ b/debian/tigr-anomaly.sgml @@ -78,7 +78,7 @@ SEE ALSO -tigr-glimmer2 (1), +tigr-glimmer3 (1), tigr-adjust (1), tigr-anomaly (1), tigr-build-icm (1), @@ -94,7 +94,7 @@ http://www.tigr.org/software/glimmer/ - Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer2. + Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer3. AUTHOR diff --git a/debian/tigr-build-icm.sgml b/debian/tigr-build-icm.sgml index 87162fc..4900485 100644 --- a/debian/tigr-build-icm.sgml +++ b/debian/tigr-build-icm.sgml @@ -74,7 +74,7 @@ Input comes from the file named on the command-line. Format should be one string per line. Each line has an ID string followed by white space -followed by the sequence itself. The script run-glimmer2 generates +followed by the sequence itself. The script run-glimmer3 generates an input file in the correct format using the 'extract' program. The IMM is constructed as follows: For a given context, say @@ -116,7 +116,7 @@ SEE ALSO -tigr-glimmer2 (1), +tigr-glimmer3 (1), tigr-long-orfs (1), tigr-adjust (1), tigr-anomaly (1), @@ -130,7 +130,7 @@ tigr-get-putative (1), http://www.tigr.org/software/glimmer/ - Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer2. + Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer3. AUTHOR diff --git a/debian/tigr-check.sgml b/debian/tigr-check.sgml index d08dce0..4106316 100644 --- a/debian/tigr-check.sgml +++ b/debian/tigr-check.sgml @@ -72,7 +72,7 @@ SEE ALSO -tigr-glimmer2 (1), +tigr-glimmer3 (1), tigr-adjust (1), tigr-anomaly (1), tigr-build-icm (1), @@ -88,7 +88,7 @@ http://www.tigr.org/software/glimmer/ - Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer2. + Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer3. AUTHOR diff --git a/debian/tigr-codon-usage.sgml b/debian/tigr-codon-usage.sgml index 58635eb..237c9eb 100644 --- a/debian/tigr-codon-usage.sgml +++ b/debian/tigr-codon-usage.sgml @@ -76,7 +76,7 @@ SEE ALSO -tigr-glimmer2 (1), +tigr-glimmer3 (1), tigr-adjust (1), tigr-anomaly (1), tigr-build-icm (1), @@ -92,7 +92,7 @@ http://www.tigr.org/software/glimmer/ - Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer2. + Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer3. AUTHOR diff --git a/debian/tigr-compare-lists.sgml b/debian/tigr-compare-lists.sgml index 7a8278c..74e7b01 100644 --- a/debian/tigr-compare-lists.sgml +++ b/debian/tigr-compare-lists.sgml @@ -76,7 +76,7 @@ SEE ALSO -tigr-glimmer2 (1), +tigr-glimmer3 (1), tigr-adjust (1), tigr-anomaly (1), tigr-build-icm (1), @@ -92,7 +92,7 @@ http://www.tigr.org/software/glimmer/ - Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer2. + Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer3. AUTHOR diff --git a/debian/tigr-extract.sgml b/debian/tigr-extract.sgml index 36449e7..465a5bb 100644 --- a/debian/tigr-extract.sgml +++ b/debian/tigr-extract.sgml @@ -116,7 +116,7 @@ SEE ALSO -tigr-glimmer2 (1), +tigr-glimmer3 (1), tigr-long-orfs (1), tigr-adjust (1), tigr-anomaly (1), @@ -133,7 +133,7 @@ http://www.tigr.org/software/glimmer/ - Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer2. + Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer3. AUTHOR diff --git a/debian/tigr-generate.sgml b/debian/tigr-generate.sgml index c3dd64f..4b664a6 100644 --- a/debian/tigr-generate.sgml +++ b/debian/tigr-generate.sgml @@ -72,7 +72,7 @@ SEE ALSO -tigr-glimmer2 (1), +tigr-glimmer3 (1), tigr-adjust (1), tigr-anomaly (1), tigr-build-icm (1), @@ -88,7 +88,7 @@ http://www.tigr.org/software/glimmer/ - Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer2. + Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer3. AUTHOR diff --git a/debian/tigr-get-len.sgml b/debian/tigr-get-len.sgml index 2fb5b80..9c40308 100644 --- a/debian/tigr-get-len.sgml +++ b/debian/tigr-get-len.sgml @@ -72,7 +72,7 @@ SEE ALSO -tigr-glimmer2 (1), +tigr-glimmer3 (1), tigr-adjust (1), tigr-anomaly (1), tigr-build-icm (1), @@ -88,7 +88,7 @@ http://www.tigr.org/software/glimmer/ - Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer2. + Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer3. AUTHOR diff --git a/debian/tigr-get-putative.sgml b/debian/tigr-get-putative.sgml index 9e8b362..8a5f0a0 100644 --- a/debian/tigr-get-putative.sgml +++ b/debian/tigr-get-putative.sgml @@ -68,7 +68,7 @@ SEE ALSO -tigr-glimmer2 (1), +tigr-glimmer3 (1), tigr-adjust (1), tigr-anomaly (1), tigr-build-icm (1), @@ -84,7 +84,7 @@ http://www.tigr.org/software/glimmer/ -Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer2. +Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer3. AUTHOR diff --git a/debian/tigr-glimmer2.sgml b/debian/tigr-glimmer2.sgml deleted file mode 100644 index 70d8e38..0000000 --- a/debian/tigr-glimmer2.sgml +++ /dev/null @@ -1,246 +0,0 @@ - manpage.1'. You may view - the manual page with: `docbook-to-man manpage.sgml | nroff -man | - less'. A typical entry in a Makefile or Makefile.am is: - -manpage.1: manpage.sgml - docbook-to-man $< > $@ - - - The docbook-to-man binary is found in the docbook-to-man package. - Please remember that if you create the nroff version in one of the - debian/rules file targets (such as build), you will need to include - docbook-to-man in your Build-Depends control field. - - --> - - - Steffen"> - Möller"> - - November 10, 2004"> - 1"> - moeller@pzr.uni-rostock.de"> - - TIGR-GLIMMER"> - - - Debian"> - GNU"> - GPL"> -]> - - - -
- &dhemail; -
- - &dhfirstname; - &dhsurname; - - - 2003 - &dhusername; - - &dhdate; - - - &dhucpackage; - - &dhsection; - - - &dhpackage; - -Find/Score potential genes in genome-file using the probability model in icm-file - - - - - tigr-glimmer2 - - - - - - - DESCRIPTION - -&dhpackage; is a system for finding genes in microbial DNA, especially the genomes of bacteria and archaea. &dhpackage; (Gene Locator and Interpolated Markov Modeler) uses interpolated Markov models (IMMs) to identify the coding regions and distinguish them from noncoding DNA. The IMM approach, described in our Nucleic Acids Research paper on &dhpackage; 1.0 and in our subsequent paper on &dhpackage; 2.0, uses a combination of Markov models from 1st through 8th-order, weighting each model according to its predictive power. &dhpackage; 1.0 and 2.0 use 3-periodic nonhomogenous Markov models in their IMMs. - -&dhpackage; is the primary microbial gene finder at TIGR, and has been used to annotate the complete genomes of B. burgdorferi (Fraser et al., Nature, Dec. 1997), T. pallidum (Fraser et al., Science, July 1998), T. maritima, D. radiodurans, M. tuberculosis, and non-TIGR projects including C. trachomatis, C. pneumoniae, and others. Its analyses of some of these genomes and others is available at the TIGR microbial database site. - -A special version of &dhpackage; designed for small eukaryotes, GlimmerM, was used to find the genes in chromosome 2 of the malaria parasite, P. falciparum.. GlimmerM is described in S.L. Salzberg, M. Pertea, A.L. Delcher, M.J. Gardner, and H. Tettelin, "Interpolated Markov models for eukaryotic gene finding," Genomics 59 (1999), 24-31. Click here (http://www.tigr.org/software/glimmerm/) to visit the GlimmerM site, which includes information on how to download the GlimmerM system. - -The &dhpackage; system consists of two main programs. The first of these is the training program, build-imm. This program takes an input set of sequences and builds and outputs the IMM for them. These sequences can be complete genes or just partial orfs. For a new genome, this training data can consist of those genes with strong database hits as well as very long open reading frames that are statistically almost certain to be genes. The second program is glimmer, which uses this IMM to identify putative genes in an entire genome. &dhpackage; automatically resolves conflicts between most overlapping genes by choosing one of them. It also identifies genes that are suspected to truly overlap, and flags these for closer inspection by the user. These ``suspect'' gene candidates have been a very small percentage of the total for all the genomes analyzed thus far. - &dhpackage; is a program that... - - - OPTIONS - - - - - Use n as GC percentage of independent model - Note: n should be a percentage, e.g., -C 45.2 - - - - -fUse ribosome-binding energy to choose start codon - - - Use first codon in orf as start codon - - - Set minimum gene length to n - - - - - Use - to select regions of bases that are off - limits, so that no bases within that area will be examined - - - - - - Assume linear rather than circular genome, i.e., no wraparound - - - - Use filename to specify a list of orfs that should - be scored separately, with no overlap rules - - - - - Input is a multifasta file of separate genes to be scored - separately, with no overlap rules - - - - - - - Set minimum overlap length to n. Overlaps shorter than this - are ignored. - - - - - - - Set minimum overlap percentage to n%. Overlaps shorter than this percentage of *both* strings are ignored. - - - - - - - Set the maximum length orf that can be rejected because of - the independent probability score column to (n - 1) - - - - - - - - Don't use independent probability score column - - - - - - -Use independent probability score column - - - - - - - - Don't use independent probability score column - - - Use string s as the ribosome binding pattern to find start codons. - - - - - - - Do use stricter independent intergenic model that doesn't - give probabilities to in-frame stop codons. (Option is obsolete - since this is now the only behaviour - - - - - - Set threshold score for calling as gene to n. If the in-frame - score >= n, then the region is given a number and considered - a potential gene. - - - - - - Use "weak" scores on tentative genes n or longer. Weak - scores ignore the independent probability score. - - - - - - SEE ALSO - -tigr-adjust (1), -tigr-anomaly (1), -tigr-build-icm (1), -tigr-check (1), -tigr-codon-usage (1), -tigr-compare-lists (1), -tigr-extract (1), -tigr-generate (1), -tigr-get-len (1), -tigr-get-putative (1), -tigr-glimmer2 (1), -tigr-long-orfs (1) - - -http://www.tigr.org/software/glimmer/ - - Please see the readme in /usr/share/doc/glimmer for a description on how to use Glimmer. - - - AUTHOR - This manual page was quickly copied from the glimmer web site by &dhusername; &dhemail; for - the &debian; system. - - - - - - - diff --git a/debian/tigr-glimmer3.sgml b/debian/tigr-glimmer3.sgml new file mode 100644 index 0000000..a011e53 --- /dev/null +++ b/debian/tigr-glimmer3.sgml @@ -0,0 +1,246 @@ + manpage.1'. You may view + the manual page with: `docbook-to-man manpage.sgml | nroff -man | + less'. A typical entry in a Makefile or Makefile.am is: + +manpage.1: manpage.sgml + docbook-to-man $< > $@ + + + The docbook-to-man binary is found in the docbook-to-man package. + Please remember that if you create the nroff version in one of the + debian/rules file targets (such as build), you will need to include + docbook-to-man in your Build-Depends control field. + + --> + + + Steffen"> + Möller"> + + November 10, 2004"> + 1"> + moeller@pzr.uni-rostock.de"> + + TIGR-GLIMMER"> + + + Debian"> + GNU"> + GPL"> +]> + + + +
+ &dhemail; +
+ + &dhfirstname; + &dhsurname; + + + 2003 + &dhusername; + + &dhdate; + + + &dhucpackage; + + &dhsection; + + + &dhpackage; + +Find/Score potential genes in genome-file using the probability model in icm-file + + + + + tigr-glimmer3 + + + + + + + DESCRIPTION + +&dhpackage; is a system for finding genes in microbial DNA, especially the genomes of bacteria and archaea. &dhpackage; (Gene Locator and Interpolated Markov Modeler) uses interpolated Markov models (IMMs) to identify the coding regions and distinguish them from noncoding DNA. The IMM approach, described in our Nucleic Acids Research paper on &dhpackage; 1.0 and in our subsequent paper on &dhpackage; 2.0, uses a combination of Markov models from 1st through 8th-order, weighting each model according to its predictive power. &dhpackage; 1.0 and 2.0 use 3-periodic nonhomogenous Markov models in their IMMs. + +&dhpackage; is the primary microbial gene finder at TIGR, and has been used to annotate the complete genomes of B. burgdorferi (Fraser et al., Nature, Dec. 1997), T. pallidum (Fraser et al., Science, July 1998), T. maritima, D. radiodurans, M. tuberculosis, and non-TIGR projects including C. trachomatis, C. pneumoniae, and others. Its analyses of some of these genomes and others is available at the TIGR microbial database site. + +A special version of &dhpackage; designed for small eukaryotes, GlimmerM, was used to find the genes in chromosome 2 of the malaria parasite, P. falciparum.. GlimmerM is described in S.L. Salzberg, M. Pertea, A.L. Delcher, M.J. Gardner, and H. Tettelin, "Interpolated Markov models for eukaryotic gene finding," Genomics 59 (1999), 24-31. Click here (http://www.tigr.org/software/glimmerm/) to visit the GlimmerM site, which includes information on how to download the GlimmerM system. + +The &dhpackage; system consists of two main programs. The first of these is the training program, build-imm. This program takes an input set of sequences and builds and outputs the IMM for them. These sequences can be complete genes or just partial orfs. For a new genome, this training data can consist of those genes with strong database hits as well as very long open reading frames that are statistically almost certain to be genes. The second program is glimmer, which uses this IMM to identify putative genes in an entire genome. &dhpackage; automatically resolves conflicts between most overlapping genes by choosing one of them. It also identifies genes that are suspected to truly overlap, and flags these for closer inspection by the user. These ``suspect'' gene candidates have been a very small percentage of the total for all the genomes analyzed thus far. + &dhpackage; is a program that... + + + OPTIONS + + + + + Use n as GC percentage of independent model + Note: n should be a percentage, e.g., -C 45.2 + + + + -fUse ribosome-binding energy to choose start codon + + + Use first codon in orf as start codon + + + Set minimum gene length to n + + + + + Use + to select regions of bases that are off + limits, so that no bases within that area will be examined + + + + + + Assume linear rather than circular genome, i.e., no wraparound + + + + Use filename to specify a list of orfs that should + be scored separately, with no overlap rules + + + + + Input is a multifasta file of separate genes to be scored + separately, with no overlap rules + + + + + + + Set minimum overlap length to n. Overlaps shorter than this + are ignored. + + + + + + + Set minimum overlap percentage to n%. Overlaps shorter than this percentage of *both* strings are ignored. + + + + + + + Set the maximum length orf that can be rejected because of + the independent probability score column to (n - 1) + + + + + + + + Don't use independent probability score column + + + + + + +Use independent probability score column + + + + + + + + Don't use independent probability score column + + + Use string s as the ribosome binding pattern to find start codons. + + + + + + + Do use stricter independent intergenic model that doesn't + give probabilities to in-frame stop codons. (Option is obsolete + since this is now the only behaviour + + + + + + Set threshold score for calling as gene to n. If the in-frame + score >= n, then the region is given a number and considered + a potential gene. + + + + + + Use "weak" scores on tentative genes n or longer. Weak + scores ignore the independent probability score. + + + + + + SEE ALSO + +tigr-adjust (1), +tigr-anomaly (1), +tigr-build-icm (1), +tigr-check (1), +tigr-codon-usage (1), +tigr-compare-lists (1), +tigr-extract (1), +tigr-generate (1), +tigr-get-len (1), +tigr-get-putative (1), +tigr-glimmer3 (1), +tigr-long-orfs (1) + + +http://www.tigr.org/software/glimmer/ + + Please see the readme in /usr/share/doc/glimmer for a description on how to use Glimmer. + + + AUTHOR + This manual page was quickly copied from the glimmer web site by &dhusername; &dhemail; for + the &debian; system. + + + + + + + diff --git a/debian/tigr-long-orfs.sgml b/debian/tigr-long-orfs.sgml index 79f5371..8d456a6 100644 --- a/debian/tigr-long-orfs.sgml +++ b/debian/tigr-long-orfs.sgml @@ -192,7 +192,7 @@ SEE ALSO -tigr-glimmer2 (1), +tigr-glimmer3 (1), tigr-adjust (1), tigr-anomaly (1), tigr-build-icm (1), @@ -208,7 +208,7 @@ http://www.tigr.org/software/glimmer/ - Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer2. + Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer3. AUTHOR diff --git a/debian/tigr-run-glimmer2.sgml b/debian/tigr-run-glimmer2.sgml deleted file mode 100644 index 2b2db86..0000000 --- a/debian/tigr-run-glimmer2.sgml +++ /dev/null @@ -1,120 +0,0 @@ - manpage.1'. You may view - the manual page with: `docbook-to-man manpage.sgml | nroff -man | - less'. A typical entry in a Makefile or Makefile.am is: - -manpage.1: manpage.sgml - docbook-to-man $< > $@ - - - The docbook-to-man binary is found in the docbook-to-man package. - Please remember that if you create the nroff version in one of the - debian/rules file targets (such as build), you will need to include - docbook-to-man in your Build-Depends control field. - - --> - - - Steffen"> - Möller"> - - November 10, 2004"> - 1"> - moeller@pzr.uni-rostock.de"> - - TIGR-GLIMMER"> - - - Debian"> - GNU"> - GPL"> -]> - - - -
- &dhemail; -
- - &dhfirstname; - &dhsurname; - - - 2003 - &dhusername; - - &dhdate; - - - &dhucpackage; - - &dhsection; - - - &dhpackage; - - -Apply the suite of programs within glimmer2 to a a prokaryotic or archean genome. - - - - - tigr-run-glimmer2 - - - - DESCRIPTION - -A shell script that wraps a set of tigr-* utilities of the glimmer package to retrieve coding regions. - - - - SEE ALSO - -tigr-glimmer2 (1), -tigr-adjust (1), -tigr-anomaly (1), -tigr-build-icm (1), -tigr-check (1), -tigr-codon-usage (1), -tigr-compare-lists (1), -tigr-extract (1), -tigr-generate (1), -tigr-get-len (1), -tigr-get-putative (1), -tigr-long-orfs (1), - - -http://www.tigr.org/software/glimmer/ - - - Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer2. - - - AUTHOR - - This manual page was quickly copied from the glimmer web site by &dhusername; &dhemail; for - the &debian; system. - - - - - - diff --git a/debian/tigr-run-glimmer3.sgml b/debian/tigr-run-glimmer3.sgml new file mode 100644 index 0000000..e460a40 --- /dev/null +++ b/debian/tigr-run-glimmer3.sgml @@ -0,0 +1,120 @@ + manpage.1'. You may view + the manual page with: `docbook-to-man manpage.sgml | nroff -man | + less'. A typical entry in a Makefile or Makefile.am is: + +manpage.1: manpage.sgml + docbook-to-man $< > $@ + + + The docbook-to-man binary is found in the docbook-to-man package. + Please remember that if you create the nroff version in one of the + debian/rules file targets (such as build), you will need to include + docbook-to-man in your Build-Depends control field. + + --> + + + Steffen"> + Möller"> + + November 10, 2004"> + 1"> + moeller@pzr.uni-rostock.de"> + + TIGR-GLIMMER"> + + + Debian"> + GNU"> + GPL"> +]> + + + +
+ &dhemail; +
+ + &dhfirstname; + &dhsurname; + + + 2003 + &dhusername; + + &dhdate; + + + &dhucpackage; + + &dhsection; + + + &dhpackage; + + +Apply the suite of programs within glimmer3 to a a prokaryotic or archean genome. + + + + + tigr-run-glimmer3 + + + + DESCRIPTION + +A shell script that wraps a set of tigr-* utilities of the glimmer package to retrieve coding regions. + + + + SEE ALSO + +tigr-glimmer3 (1), +tigr-adjust (1), +tigr-anomaly (1), +tigr-build-icm (1), +tigr-check (1), +tigr-codon-usage (1), +tigr-compare-lists (1), +tigr-extract (1), +tigr-generate (1), +tigr-get-len (1), +tigr-get-putative (1), +tigr-long-orfs (1), + + +http://www.tigr.org/software/glimmer/ + + + Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer3. + + + AUTHOR + + This manual page was quickly copied from the glimmer web site by &dhusername; &dhemail; for + the &debian; system. + + + + + +