Package list tigr-glimmer / 74d6398
Fixing version number in manpages Andreas Tille 13 years ago
19 changed file(s) with 532 addition(s) and 544 deletion(s). Raw diff Collapse all Expand all
44 DM-Upload-Allowed: yes
55 Uploaders: Steffen Moeller <moeller@debian.org>,
66 Andreas Tille <tille@debian.org>
7 Build-Depends: debhelper (>= 5.0), docbook-to-man, gzip, cdbs, quilt
7 Build-Depends: debhelper (>= 5.0), docbook-to-man, cdbs, quilt
88 Standards-Version: 3.7.3
99 Homepage: http://www.tigr.org/software/glimmer/
1010 Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/tigr-glimmer/trunk/?rev=0&sc=0
4848 .ds f2\"
4949 .ds f3\"
5050 .ds f4\"
51 '\" t
52 .ta 8n 16n 24n 32n 40n 48n 56n 64n 72n
53 .TH "LONG-ORFS" "1"
54 .SH "NAME"
55 long-orfs \(em Find/Score potential genes in genome-file using
56 the probability model in icm-file
57 .SH "SYNOPSIS"
58 .PP
59 \fBlong-orgs\fR [genome-file \fB\fIoptions\fR\fP]
60 .SH "DESCRIPTION"
61 .PP
62 Program long-orfs takes a sequence file (in FASTA format) and
63 outputs a list of all long "potential genes" in it that do not
64 overlap by too much. By "potential gene" I mean the portion of
65 an orf from the first start codon to the stop codon at the end.
66 .PP
67 The first few lines of output specify the settings of various
68 parameters in the program:
69 .PP
70 Minimum gene length is the length of the smallest fragment
71 considered to be a gene. The length is measured from the first base
72 of the start codon to the last base *before* the stop codon.
73 This value can be specified when running the program with the -g option.
74 By default, the program now (April 2003) will compute an optimal length
75 for this parameter, where "optimal" is the value that produces the
76 greatest number of long ORFs, thereby increasing the amount of data
77 used for training.
78 .PP
79 Minimum overlap length is a lower bound on the number of bases overlap
80 between 2 genes that is considered a problem. Overlaps shorter than
81 this are ignored.
82 .PP
83 Minimum overlap percent is another lower bound on the number of bases
84 overlap that is considered a problem. Overlaps shorter than this
85 percentage of *both* genes are ignored.
86 .PP
87 The next portion of the output is a list of potential genes:
88 .PP
89 Column 1 is an ID number for reference purposes. It is assigned
90 sequentially starting with 1 to all long potential genes. If
91 overlapping genes are eliminated, gaps in the numbers will occur.
92 The ID prefix is specified in the constant ID_PREFIX .
93 .PP
94 Column 2 is the position of the first base of the first start codon in
95 the orf. Currently I use atg, and gtg as start codons. This is
96 easily changed in the function Is_Start () .
97 .PP
98 Column 3 is the position of the last base *before* the stop codon. Stop
99 codons are taa, tag, and tga. Note that for orfs in the reverse
100 reading frames have their start position higher than the end position.
101 The order in which orfs are listed is in increasing order by
102 Max {OrfStart, End}, i.e., the highest numbered position in the orf,
103 except for orfs that "wrap around" the end of the sequence.
104 .PP
105 When two genes with ID numbers overlap by at least a sufficient
106 amount (as determined by Min_Olap and Min_Olap_Percent ), they
107 are eliminated and do not appear in the output.
108 .PP
109 The final output of the program (sent to the standard error file so
110 it does not show up when output is redirected to a file) is the
111 length of the longest orf found.
112 .PP
113
114 Specifying Different Start and Stop Codons:
115 .PP
116 To specify different sets of start and stop codons, modify the file
117 gene.h . Specifically, the functions:
118 .PP
119 Is_Forward_Start Is_Reverse_Start Is_Start
120 Is_Forward_Stop Is_Reverse_Stop Is_Stop
121 .PP
122 are used to determine what is used for start and stop codons.
123 .PP
124 Is_Start and Is_Stop do simple string comparisons to specify
125 which patterns are used. To add a new pattern, just add the comparison
126 for it. To remove a pattern, comment out or delete the comparison
127 for it.
128 .PP
129 The other four functions use a bit comparison to determine start and
130 stop patterns. They represent a codon as a 12-bit pattern, with 4 bits
131 for each base, one bit for each possible value of the bases, T, G, C
132 or A. Thus the bit pattern 0010 0101 1100 represents the base
133 pattern [C] [A or G] [G or T]. By doing bit operations (& | ~) and
134 comparisons, more complicated patterns involving ambiguous reads
135 can be tested efficiently. Simple patterns can be tested as in
136 the current code.
137 .PP
138 For example, to insert an additional start codon of CAT requires 3 changes:
139 1. The line
140 || (Codon & 0x218) == Codon
141 should be inserted into Is_Forward_Start , since 0x218 = 0010 0001 1000
142 represents CAT.
143 2. The line
144 || (Codon & 0x184) == Codon
145 should be inserted into Is_Reverse_Start , since 0x184 = 0001 1000 0100
146 represents ATG, which is the reverse-complement of CAT. Alternately,
147 the #define constant ATG_MASK could be used.
148 3. The line
149 || strncmp (S, "cat", 3) == 0
150 should be inserted into Is_Start .
151 .SH "OPTIONS"
152 .IP "\fB-g \fIn\fR\fP" 10
153 Set minimum gene length to n. Default is to compute an
154 optimal value automatically. Don't change this unless you
155 know what you're doing.
156 .IP "\fB-l\fP" 10
157 Regard the genome as linear (not circular), i.e., do not allow
158 genes to "wrap around" the end of the genome.
159 This option works on both glimmer and long-orfs .
160 The default behavior is to regard the genome as circular.
161 .IP "\fB-o \fIn\fR\fP" 10
162 Set maximum overlap length to n. Overlaps shorter than this
163 are permitted. (Default is 0 bp.)
164 .IP "\fB-p \fIn\fR\fP" 10
165 Set maximum overlap percentage to n%. Overlaps shorter than
166 this percentage of *both* strings are ignored. (Default is 10%.)
167 .SH "SEE ALSO"
168 .PP
169 glimmer2 (1),
170 adjust (1),
171 anomaly (1),
172 build-icm (1),
173 check (1),
174 codon-usage (1),
175 compare-lists (1),
176 extract (1),
177 generate (1),
178 get-len (1),
179 get-putative (1),
180 .PP
181 http://www.tigr.org/software/glimmer/
182 .PP
183 Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer2.
184 .SH "AUTHOR"
185 .PP
186 This manual page was quickly copied from the glimmer web site by Steffen Moeller moeller@pzr.uni-rostock.de for
187 the \fBDebian\fP system.
188
189 ...\" created by instant / docbook-to-man, Sun 09 Nov 2003, 19:43
51 '\" t
52 .ta 8n 16n 24n 32n 40n 48n 56n 64n 72n
53 .TH "LONG-ORFS" "1"
54 .SH "NAME"
55 long-orfs \(em Find/Score potential genes in genome-file using
56 the probability model in icm-file
57 .SH "SYNOPSIS"
58 .PP
59 \fBlong-orgs\fR [genome-file \fB\fIoptions\fR\fP]
60 .SH "DESCRIPTION"
61 .PP
62 Program long-orfs takes a sequence file (in FASTA format) and
63 outputs a list of all long "potential genes" in it that do not
64 overlap by too much. By "potential gene" I mean the portion of
65 an orf from the first start codon to the stop codon at the end.
66 .PP
67 The first few lines of output specify the settings of various
68 parameters in the program:
69 .PP
70 Minimum gene length is the length of the smallest fragment
71 considered to be a gene. The length is measured from the first base
72 of the start codon to the last base *before* the stop codon.
73 This value can be specified when running the program with the -g option.
74 By default, the program now (April 2003) will compute an optimal length
75 for this parameter, where "optimal" is the value that produces the
76 greatest number of long ORFs, thereby increasing the amount of data
77 used for training.
78 .PP
79 Minimum overlap length is a lower bound on the number of bases overlap
80 between 2 genes that is considered a problem. Overlaps shorter than
81 this are ignored.
82 .PP
83 Minimum overlap percent is another lower bound on the number of bases
84 overlap that is considered a problem. Overlaps shorter than this
85 percentage of *both* genes are ignored.
86 .PP
87 The next portion of the output is a list of potential genes:
88 .PP
89 Column 1 is an ID number for reference purposes. It is assigned
90 sequentially starting with 1 to all long potential genes. If
91 overlapping genes are eliminated, gaps in the numbers will occur.
92 The ID prefix is specified in the constant ID_PREFIX .
93 .PP
94 Column 2 is the position of the first base of the first start codon in
95 the orf. Currently I use atg, and gtg as start codons. This is
96 easily changed in the function Is_Start () .
97 .PP
98 Column 3 is the position of the last base *before* the stop codon. Stop
99 codons are taa, tag, and tga. Note that for orfs in the reverse
100 reading frames have their start position higher than the end position.
101 The order in which orfs are listed is in increasing order by
102 Max {OrfStart, End}, i.e., the highest numbered position in the orf,
103 except for orfs that "wrap around" the end of the sequence.
104 .PP
105 When two genes with ID numbers overlap by at least a sufficient
106 amount (as determined by Min_Olap and Min_Olap_Percent ), they
107 are eliminated and do not appear in the output.
108 .PP
109 The final output of the program (sent to the standard error file so
110 it does not show up when output is redirected to a file) is the
111 length of the longest orf found.
112 .PP
113
114 Specifying Different Start and Stop Codons:
115 .PP
116 To specify different sets of start and stop codons, modify the file
117 gene.h . Specifically, the functions:
118 .PP
119 Is_Forward_Start Is_Reverse_Start Is_Start
120 Is_Forward_Stop Is_Reverse_Stop Is_Stop
121 .PP
122 are used to determine what is used for start and stop codons.
123 .PP
124 Is_Start and Is_Stop do simple string comparisons to specify
125 which patterns are used. To add a new pattern, just add the comparison
126 for it. To remove a pattern, comment out or delete the comparison
127 for it.
128 .PP
129 The other four functions use a bit comparison to determine start and
130 stop patterns. They represent a codon as a 12-bit pattern, with 4 bits
131 for each base, one bit for each possible value of the bases, T, G, C
132 or A. Thus the bit pattern 0010 0101 1100 represents the base
133 pattern [C] [A or G] [G or T]. By doing bit operations (& | ~) and
134 comparisons, more complicated patterns involving ambiguous reads
135 can be tested efficiently. Simple patterns can be tested as in
136 the current code.
137 .PP
138 For example, to insert an additional start codon of CAT requires 3 changes:
139 1. The line
140 || (Codon & 0x218) == Codon
141 should be inserted into Is_Forward_Start , since 0x218 = 0010 0001 1000
142 represents CAT.
143 2. The line
144 || (Codon & 0x184) == Codon
145 should be inserted into Is_Reverse_Start , since 0x184 = 0001 1000 0100
146 represents ATG, which is the reverse-complement of CAT. Alternately,
147 the #define constant ATG_MASK could be used.
148 3. The line
149 || strncmp (S, "cat", 3) == 0
150 should be inserted into Is_Start .
151 .SH "OPTIONS"
152 .IP "\fB-g \fIn\fR\fP" 10
153 Set minimum gene length to n. Default is to compute an
154 optimal value automatically. Don't change this unless you
155 know what you're doing.
156 .IP "\fB-l\fP" 10
157 Regard the genome as linear (not circular), i.e., do not allow
158 genes to "wrap around" the end of the genome.
159 This option works on both glimmer and long-orfs .
160 The default behavior is to regard the genome as circular.
161 .IP "\fB-o \fIn\fR\fP" 10
162 Set maximum overlap length to n. Overlaps shorter than this
163 are permitted. (Default is 0 bp.)
164 .IP "\fB-p \fIn\fR\fP" 10
165 Set maximum overlap percentage to n%. Overlaps shorter than
166 this percentage of *both* strings are ignored. (Default is 10%.)
167 .SH "SEE ALSO"
168 .PP
169 glimmer3 (1),
170 adjust (1),
171 anomaly (1),
172 build-icm (1),
173 check (1),
174 codon-usage (1),
175 compare-lists (1),
176 extract (1),
177 generate (1),
178 get-len (1),
179 get-putative (1),
180 .PP
181 http://www.tigr.org/software/glimmer/
182 .PP
183 Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer3.
184 .SH "AUTHOR"
185 .PP
186 This manual page was quickly copied from the glimmer web site by Steffen Moeller moeller@pzr.uni-rostock.de for
187 the \fBDebian\fP system.
188
189 ...\" created by instant / docbook-to-man, Sun 09 Nov 2003, 19:43
0 debian/tigr-adjust.1
1 debian/tigr-anomaly.1
2 debian/tigr-build-icm.1
3 debian/tigr-check.1
4 debian/tigr-codon-usage.1
5 debian/tigr-compare-lists.1
6 debian/tigr-extract.1
7 debian/tigr-generate.1
8 debian/tigr-get-len.1
9 debian/tigr-get-putative.1
10 debian/tigr-glimmer2.1
11 debian/tigr-long-orfs.1
12 debian/tigr-run-glimmer2.1
0 debian/tigr-*.1
55 include /usr/share/cdbs/1/rules/debhelper.mk
66 include /usr/share/cdbs/1/class/makefile.mk
77
8 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
8 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
99
1010 .SUFFIXES: .1 .sgml
1111
1313 docbook-to-man $< > $@
1414
1515 clean::
16 dh_clean $(MANPAGES) tigr-run-glimmer2
16 dh_clean $(MANPAGES)
1717 rm -f bin/* lib/* obj/*
1818
1919 build/tigr-glimmer:: $(MANPAGES)
7171 <refsect1>
7272 <title>SEE ALSO</title>
7373 <para>
74 tigr-glimmer2 (1),
74 tigr-glimmer3 (1),
7575 tigr-adjust (1),
7676 tigr-anomaly (1),
7777 tigr-build-icm (1),
8888 http://www.tigr.org/software/glimmer/
8989 </para>
9090
91 <para>Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer2.</para>
91 <para>Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer3.</para>
9292 </refsect1>
9393 <refsect1>
9494 <title>AUTHOR</title>
7777 <refsect1>
7878 <title>SEE ALSO</title>
7979 <para>
80 tigr-glimmer2 (1),
80 tigr-glimmer3 (1),
8181 tigr-adjust (1),
8282 tigr-anomaly (1),
8383 tigr-build-icm (1),
9393 http://www.tigr.org/software/glimmer/
9494 </para>
9595
96 <para>Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer2.</para>
96 <para>Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer3.</para>
9797 </refsect1>
9898 <refsect1>
9999 <title>AUTHOR</title>
7373 </para><para>
7474 Input comes from the file named on the command-line. Format should be
7575 one string per line. Each line has an ID string followed by white space
76 followed by the sequence itself. The script run-glimmer2 generates
76 followed by the sequence itself. The script run-glimmer3 generates
7777 an input file in the correct format using the 'extract' program.
7878 </para><para>
7979 The IMM is constructed as follows: For a given context, say
115115 <refsect1>
116116 <title>SEE ALSO</title>
117117 <para>
118 tigr-glimmer2 (1),
118 tigr-glimmer3 (1),
119119 tigr-long-orfs (1),
120120 tigr-adjust (1),
121121 tigr-anomaly (1),
129129 tigr-get-putative (1),
130130 </para>
131131 <para>http://www.tigr.org/software/glimmer/</para>
132 <para>Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer2.</para>
132 <para>Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer3.</para>
133133 </refsect1>
134134 <refsect1>
135135 <title>AUTHOR</title>
7171 <refsect1>
7272 <title>SEE ALSO</title>
7373 <para>
74 tigr-glimmer2 (1),
74 tigr-glimmer3 (1),
7575 tigr-adjust (1),
7676 tigr-anomaly (1),
7777 tigr-build-icm (1),
8787 http://www.tigr.org/software/glimmer/
8888 </para>
8989
90 <para>Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer2.</para>
90 <para>Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer3.</para>
9191 </refsect1>
9292 <refsect1>
9393 <title>AUTHOR</title>
7575 <refsect1>
7676 <title>SEE ALSO</title>
7777 <para>
78 tigr-glimmer2 (1),
78 tigr-glimmer3 (1),
7979 tigr-adjust (1),
8080 tigr-anomaly (1),
8181 tigr-build-icm (1),
9191 http://www.tigr.org/software/glimmer/
9292 </para>
9393
94 <para>Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer2.</para>
94 <para>Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer3.</para>
9595 </refsect1>
9696 <refsect1>
9797 <title>AUTHOR</title>
7575 <refsect1>
7676 <title>SEE ALSO</title>
7777 <para>
78 tigr-glimmer2 (1),
78 tigr-glimmer3 (1),
7979 tigr-adjust (1),
8080 tigr-anomaly (1),
8181 tigr-build-icm (1),
9191 http://www.tigr.org/software/glimmer/
9292 </para>
9393
94 <para>Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer2.</para>
94 <para>Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer3.</para>
9595 </refsect1>
9696 <refsect1>
9797 <title>AUTHOR</title>
115115 <refsect1>
116116 <title>SEE ALSO</title>
117117 <para>
118 tigr-glimmer2 (1),
118 tigr-glimmer3 (1),
119119 tigr-long-orfs (1),
120120 tigr-adjust (1),
121121 tigr-anomaly (1),
132132 http://www.tigr.org/software/glimmer/
133133 </para>
134134
135 <para>Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer2.</para>
135 <para>Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer3.</para>
136136 </refsect1>
137137 <refsect1>
138138 <title>AUTHOR</title>
7171 <refsect1>
7272 <title>SEE ALSO</title>
7373 <para>
74 tigr-glimmer2 (1),
74 tigr-glimmer3 (1),
7575 tigr-adjust (1),
7676 tigr-anomaly (1),
7777 tigr-build-icm (1),
8787 http://www.tigr.org/software/glimmer/
8888 </para>
8989
90 <para>Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer2.</para>
90 <para>Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer3.</para>
9191 </refsect1>
9292 <refsect1>
9393 <title>AUTHOR</title>
7171 <refsect1>
7272 <title>SEE ALSO</title>
7373 <para>
74 tigr-glimmer2 (1),
74 tigr-glimmer3 (1),
7575 tigr-adjust (1),
7676 tigr-anomaly (1),
7777 tigr-build-icm (1),
8787 http://www.tigr.org/software/glimmer/
8888 </para>
8989
90 <para>Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer2.</para>
90 <para>Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer3.</para>
9191 </refsect1>
9292 <refsect1>
9393 <title>AUTHOR</title>
6767 <refsect1>
6868 <title>SEE ALSO</title>
6969 <para>
70 tigr-glimmer2 (1),
70 tigr-glimmer3 (1),
7171 tigr-adjust (1),
7272 tigr-anomaly (1),
7373 tigr-build-icm (1),
8383 <para>
8484 http://www.tigr.org/software/glimmer/
8585 </para>
86 <para>Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer2.</para>
86 <para>Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer3.</para>
8787 </refsect1>
8888 <refsect1>
8989 <title>AUTHOR</title>
+0
-246
debian/tigr-glimmer2.sgml less more
0 <!doctype refentry PUBLIC "-//OASIS//DTD DocBook V4.1//EN" [
1
2 <!-- Process this file with docbook-to-man to generate an nroff manual
3 page: `docbook-to-man manpage.sgml > manpage.1'. You may view
4 the manual page with: `docbook-to-man manpage.sgml | nroff -man |
5 less'. A typical entry in a Makefile or Makefile.am is:
6
7 manpage.1: manpage.sgml
8 docbook-to-man $< > $@
9
10
11 The docbook-to-man binary is found in the docbook-to-man package.
12 Please remember that if you create the nroff version in one of the
13 debian/rules file targets (such as build), you will need to include
14 docbook-to-man in your Build-Depends control field.
15
16 -->
17
18 <!-- Fill in your name for FIRSTNAME and SURNAME. -->
19 <!ENTITY dhfirstname "<firstname>Steffen</firstname>">
20 <!ENTITY dhsurname "<surname>Möller</surname>">
21 <!-- Please adjust the date whenever revising the manpage. -->
22 <!ENTITY dhdate "<date>November 10, 2004</date>">
23 <!ENTITY dhsection "<manvolnum>1</manvolnum>">
24 <!ENTITY dhemail "<email>moeller@pzr.uni-rostock.de</email>">
25 <!ENTITY dhusername "Steffen Moeller">
26 <!ENTITY dhucpackage "<refentrytitle>TIGR-GLIMMER</refentrytitle>">
27 <!ENTITY dhpackage "tigr-glimmer">
28
29 <!ENTITY debian "<productname>Debian</productname>">
30 <!ENTITY gnu "<acronym>GNU</acronym>">
31 <!ENTITY gpl "&gnu; <acronym>GPL</acronym>">
32 ]>
33
34 <refentry>
35 <refentryinfo>
36 <address>
37 &dhemail;
38 </address>
39 <author>
40 &dhfirstname;
41 &dhsurname;
42 </author>
43 <copyright>
44 <year>2003</year>
45 <holder>&dhusername;</holder>
46 </copyright>
47 &dhdate;
48 </refentryinfo>
49 <refmeta>
50 &dhucpackage;
51
52 &dhsection;
53 </refmeta>
54 <refnamediv>
55 <refname>&dhpackage;</refname>
56 <refpurpose>
57 Find/Score potential genes in genome-file using the probability model in icm-file
58 </refpurpose>
59 </refnamediv>
60 <refsynopsisdiv>
61 <cmdsynopsis>
62 <command>tigr-glimmer2</command>
63 <arg><option><replaceable>genome-file</replaceable></option></arg>
64 <arg><option><replaceable>icm-file</replaceable></option></arg>
65 <arg><option><replaceable>[options]</replaceable></option></arg>
66 </cmdsynopsis>
67 </refsynopsisdiv>
68 <refsect1>
69 <title>DESCRIPTION</title>
70 <para>
71 <command>&dhpackage;</command> is a system for finding genes in microbial DNA, especially the genomes of bacteria and archaea. <command>&dhpackage;</command> (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 <command>&dhpackage;</command> 1.0 and in our subsequent paper on <command>&dhpackage;</command> 2.0, uses a combination of Markov models from 1st through 8th-order, weighting each model according to its predictive power. <command>&dhpackage;</command> 1.0 and 2.0 use 3-periodic nonhomogenous Markov models in their IMMs.
72 </para><para>
73 <command>&dhpackage;</command> 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.
74 </para><para>
75 A special version of <command>&dhpackage;</command> 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.
76 </para><para>
77 The <command>&dhpackage;</command> 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. <command>&dhpackage;</command> 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.
78 <command>&dhpackage;</command> is a program that...</para>
79 </refsect1>
80 <refsect1>
81 <title>OPTIONS</title>
82 <variablelist>
83 <varlistentry>
84 <term><option>-C <replaceable>n</replaceable></option></term>
85 <listitem>
86 <para>Use n as GC percentage of independent model</para>
87 <para>Note: n should be a percentage, e.g., -C 45.2</para>
88 </listitem>
89 </varlistentry>
90 <varlistentry>
91 <term>-f</term><listitem><para>Use ribosome-binding energy to choose start codon</para></listitem>
92 </varlistentry>
93 <varlistentry>
94 <term><option>+f</option></term><listitem><para>Use first codon in orf as start codon</para></listitem>
95 </varlistentry>
96 <varlistentry>
97 <term><option>-g <replaceable>n</replaceable></option></term><listitem><para>Set minimum gene length to n</para></listitem>
98 </varlistentry>
99 <varlistentry>
100 <term><option>-i <replaceable>filename</replaceable></option></term>
101 <listitem>
102 <para>Use <option><replaceable>filename</replaceable></option>
103 to select regions of bases that are off
104 limits, so that no bases within that area will be examined
105 </para>
106 </listitem>
107 </varlistentry>
108 <varlistentry>
109 <term><option>-l</option></term>
110 <listitem><para>Assume linear rather than circular genome, i.e., no wraparound</para></listitem>
111 </varlistentry>
112 <varlistentry>
113 <term><option>-L <replaceable>filename</replaceable></option></term>
114 <listitem><para>Use filename to specify a list of orfs that should
115 be scored separately, with no overlap rules
116 </para></listitem>
117 </varlistentry>
118 <varlistentry>
119 <term><option>-M</option></term>
120 <listitem><para>Input is a multifasta file of separate genes to be scored
121 separately, with no overlap rules
122 </para>
123 </listitem>
124 </varlistentry>
125 <varlistentry>
126 <term><option>-o <replaceable>n</replaceable></option></term>
127 <listitem>
128 <para>Set minimum overlap length to n. Overlaps shorter than this
129 are ignored.
130 </para></listitem>
131 </varlistentry>
132 <varlistentry>
133 <term><option>-p <replaceable>n</replaceable></option></term>
134 <listitem>
135 <para>
136 Set minimum overlap percentage to n%. Overlaps shorter than this percentage of *both* strings are ignored.
137 </para>
138 </listitem>
139 </varlistentry>
140 <varlistentry>
141 <term><option>-q <replaceable>n</replaceable></option></term>
142 <listitem>
143 <para>Set the maximum length orf that can be rejected because of
144 the independent probability score column to (n - 1)
145 </para>
146 </listitem>
147 </varlistentry>
148 <varlistentry>
149 <term><option>-r</option></term>
150 <listitem>
151 <para>
152 Don't use independent probability score column
153 </para>
154 </listitem>
155 </varlistentry>
156 <varlistentry>
157 <term><option>+r</option></term>
158 <listitem><para>
159 Use independent probability score column
160 </para>
161 </listitem>
162 </varlistentry>
163 <varlistentry>
164 <term><option>-r</option></term>
165 <listitem>
166 <para>
167 Don't use independent probability score column
168 </para> </listitem> </varlistentry> <varlistentry>
169 <term><option>-s <replaceable>s</replaceable></option></term>
170 <listitem><para> Use string s as the ribosome binding pattern to find start codons.</para>
171 </listitem>
172 </varlistentry>
173 <varlistentry>
174 <term><option>+S</option></term>
175 <listitem>
176 <para>
177 Do use stricter independent intergenic model that doesn't
178 give probabilities to in-frame stop codons. (Option is obsolete
179 since this is now the only behaviour
180 </para> </listitem>
181 </varlistentry>
182 <varlistentry>
183 <term><option>-t <replaceable>n</replaceable></option></term>
184 <listitem><para>
185 Set threshold score for calling as gene to n. If the in-frame
186 score >= n, then the region is given a number and considered
187 a potential gene.
188 </para> </listitem>
189 </varlistentry>
190 <varlistentry>
191 <term><option>-w <replaceable>n</replaceable> </option></term>
192 <listitem><para>
193 Use "weak" scores on tentative genes n or longer. Weak
194 scores ignore the independent probability score.
195 </para></listitem>
196 </varlistentry>
197 </variablelist>
198 </refsect1>
199 <refsect1>
200 <title>SEE ALSO</title>
201 <para>
202 tigr-adjust (1),
203 tigr-anomaly (1),
204 tigr-build-icm (1),
205 tigr-check (1),
206 tigr-codon-usage (1),
207 tigr-compare-lists (1),
208 tigr-extract (1),
209 tigr-generate (1),
210 tigr-get-len (1),
211 tigr-get-putative (1),
212 tigr-glimmer2 (1),
213 tigr-long-orfs (1)
214 </para>
215 <para>
216 http://www.tigr.org/software/glimmer/
217 </para>
218 <para>Please see the readme in /usr/share/doc/glimmer for a description on how to use Glimmer.</para>
219 </refsect1>
220 <refsect1>
221 <title>AUTHOR</title>
222 <para>This manual page was quickly copied from the glimmer web site by &dhusername; &dhemail; for
223 the &debian; system.
224 </para>
225 </refsect1>
226 </refentry>
227
228 <!-- Keep this comment at the end of the file
229 Local variables:
230 mode: sgml
231 sgml-omittag:t
232 sgml-shorttag:t
233 sgml-minimize-attributes:nil
234 sgml-always-quote-attributes:t
235 sgml-indent-step:2
236 sgml-indent-data:t
237 sgml-parent-document:nil
238 sgml-default-dtd-file:nil
239 sgml-exposed-tags:nil
240 sgml-local-catalogs:nil
241 sgml-local-ecat-files:nil
242 End:
243 -->
244
245
0 <!doctype refentry PUBLIC "-//OASIS//DTD DocBook V4.1//EN" [
1
2 <!-- Process this file with docbook-to-man to generate an nroff manual
3 page: `docbook-to-man manpage.sgml > manpage.1'. You may view
4 the manual page with: `docbook-to-man manpage.sgml | nroff -man |
5 less'. A typical entry in a Makefile or Makefile.am is:
6
7 manpage.1: manpage.sgml
8 docbook-to-man $< > $@
9
10
11 The docbook-to-man binary is found in the docbook-to-man package.
12 Please remember that if you create the nroff version in one of the
13 debian/rules file targets (such as build), you will need to include
14 docbook-to-man in your Build-Depends control field.
15
16 -->
17
18 <!-- Fill in your name for FIRSTNAME and SURNAME. -->
19 <!ENTITY dhfirstname "<firstname>Steffen</firstname>">
20 <!ENTITY dhsurname "<surname>Möller</surname>">
21 <!-- Please adjust the date whenever revising the manpage. -->
22 <!ENTITY dhdate "<date>November 10, 2004</date>">
23 <!ENTITY dhsection "<manvolnum>1</manvolnum>">
24 <!ENTITY dhemail "<email>moeller@pzr.uni-rostock.de</email>">
25 <!ENTITY dhusername "Steffen Moeller">
26 <!ENTITY dhucpackage "<refentrytitle>TIGR-GLIMMER</refentrytitle>">
27 <!ENTITY dhpackage "tigr-glimmer">
28
29 <!ENTITY debian "<productname>Debian</productname>">
30 <!ENTITY gnu "<acronym>GNU</acronym>">
31 <!ENTITY gpl "&gnu; <acronym>GPL</acronym>">
32 ]>
33
34 <refentry>
35 <refentryinfo>
36 <address>
37 &dhemail;
38 </address>
39 <author>
40 &dhfirstname;
41 &dhsurname;
42 </author>
43 <copyright>
44 <year>2003</year>
45 <holder>&dhusername;</holder>
46 </copyright>
47 &dhdate;
48 </refentryinfo>
49 <refmeta>
50 &dhucpackage;
51
52 &dhsection;
53 </refmeta>
54 <refnamediv>
55 <refname>&dhpackage;</refname>
56 <refpurpose>
57 Find/Score potential genes in genome-file using the probability model in icm-file
58 </refpurpose>
59 </refnamediv>
60 <refsynopsisdiv>
61 <cmdsynopsis>
62 <command>tigr-glimmer3</command>
63 <arg><option><replaceable>genome-file</replaceable></option></arg>
64 <arg><option><replaceable>icm-file</replaceable></option></arg>
65 <arg><option><replaceable>[options]</replaceable></option></arg>
66 </cmdsynopsis>
67 </refsynopsisdiv>
68 <refsect1>
69 <title>DESCRIPTION</title>
70 <para>
71 <command>&dhpackage;</command> is a system for finding genes in microbial DNA, especially the genomes of bacteria and archaea. <command>&dhpackage;</command> (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 <command>&dhpackage;</command> 1.0 and in our subsequent paper on <command>&dhpackage;</command> 2.0, uses a combination of Markov models from 1st through 8th-order, weighting each model according to its predictive power. <command>&dhpackage;</command> 1.0 and 2.0 use 3-periodic nonhomogenous Markov models in their IMMs.
72 </para><para>
73 <command>&dhpackage;</command> 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.
74 </para><para>
75 A special version of <command>&dhpackage;</command> 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.
76 </para><para>
77 The <command>&dhpackage;</command> 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. <command>&dhpackage;</command> 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.
78 <command>&dhpackage;</command> is a program that...</para>
79 </refsect1>
80 <refsect1>
81 <title>OPTIONS</title>
82 <variablelist>
83 <varlistentry>
84 <term><option>-C <replaceable>n</replaceable></option></term>
85 <listitem>
86 <para>Use n as GC percentage of independent model</para>
87 <para>Note: n should be a percentage, e.g., -C 45.2</para>
88 </listitem>
89 </varlistentry>
90 <varlistentry>
91 <term>-f</term><listitem><para>Use ribosome-binding energy to choose start codon</para></listitem>
92 </varlistentry>
93 <varlistentry>
94 <term><option>+f</option></term><listitem><para>Use first codon in orf as start codon</para></listitem>
95 </varlistentry>
96 <varlistentry>
97 <term><option>-g <replaceable>n</replaceable></option></term><listitem><para>Set minimum gene length to n</para></listitem>
98 </varlistentry>
99 <varlistentry>
100 <term><option>-i <replaceable>filename</replaceable></option></term>
101 <listitem>
102 <para>Use <option><replaceable>filename</replaceable></option>
103 to select regions of bases that are off
104 limits, so that no bases within that area will be examined
105 </para>
106 </listitem>
107 </varlistentry>
108 <varlistentry>
109 <term><option>-l</option></term>
110 <listitem><para>Assume linear rather than circular genome, i.e., no wraparound</para></listitem>
111 </varlistentry>
112 <varlistentry>
113 <term><option>-L <replaceable>filename</replaceable></option></term>
114 <listitem><para>Use filename to specify a list of orfs that should
115 be scored separately, with no overlap rules
116 </para></listitem>
117 </varlistentry>
118 <varlistentry>
119 <term><option>-M</option></term>
120 <listitem><para>Input is a multifasta file of separate genes to be scored
121 separately, with no overlap rules
122 </para>
123 </listitem>
124 </varlistentry>
125 <varlistentry>
126 <term><option>-o <replaceable>n</replaceable></option></term>
127 <listitem>
128 <para>Set minimum overlap length to n. Overlaps shorter than this
129 are ignored.
130 </para></listitem>
131 </varlistentry>
132 <varlistentry>
133 <term><option>-p <replaceable>n</replaceable></option></term>
134 <listitem>
135 <para>
136 Set minimum overlap percentage to n%. Overlaps shorter than this percentage of *both* strings are ignored.
137 </para>
138 </listitem>
139 </varlistentry>
140 <varlistentry>
141 <term><option>-q <replaceable>n</replaceable></option></term>
142 <listitem>
143 <para>Set the maximum length orf that can be rejected because of
144 the independent probability score column to (n - 1)
145 </para>
146 </listitem>
147 </varlistentry>
148 <varlistentry>
149 <term><option>-r</option></term>
150 <listitem>
151 <para>
152 Don't use independent probability score column
153 </para>
154 </listitem>
155 </varlistentry>
156 <varlistentry>
157 <term><option>+r</option></term>
158 <listitem><para>
159 Use independent probability score column
160 </para>
161 </listitem>
162 </varlistentry>
163 <varlistentry>
164 <term><option>-r</option></term>
165 <listitem>
166 <para>
167 Don't use independent probability score column
168 </para> </listitem> </varlistentry> <varlistentry>
169 <term><option>-s <replaceable>s</replaceable></option></term>
170 <listitem><para> Use string s as the ribosome binding pattern to find start codons.</para>
171 </listitem>
172 </varlistentry>
173 <varlistentry>
174 <term><option>+S</option></term>
175 <listitem>
176 <para>
177 Do use stricter independent intergenic model that doesn't
178 give probabilities to in-frame stop codons. (Option is obsolete
179 since this is now the only behaviour
180 </para> </listitem>
181 </varlistentry>
182 <varlistentry>
183 <term><option>-t <replaceable>n</replaceable></option></term>
184 <listitem><para>
185 Set threshold score for calling as gene to n. If the in-frame
186 score >= n, then the region is given a number and considered
187 a potential gene.
188 </para> </listitem>
189 </varlistentry>
190 <varlistentry>
191 <term><option>-w <replaceable>n</replaceable> </option></term>
192 <listitem><para>
193 Use "weak" scores on tentative genes n or longer. Weak
194 scores ignore the independent probability score.
195 </para></listitem>
196 </varlistentry>
197 </variablelist>
198 </refsect1>
199 <refsect1>
200 <title>SEE ALSO</title>
201 <para>
202 tigr-adjust (1),
203 tigr-anomaly (1),
204 tigr-build-icm (1),
205 tigr-check (1),
206 tigr-codon-usage (1),
207 tigr-compare-lists (1),
208 tigr-extract (1),
209 tigr-generate (1),
210 tigr-get-len (1),
211 tigr-get-putative (1),
212 tigr-glimmer3 (1),
213 tigr-long-orfs (1)
214 </para>
215 <para>
216 http://www.tigr.org/software/glimmer/
217 </para>
218 <para>Please see the readme in /usr/share/doc/glimmer for a description on how to use Glimmer.</para>
219 </refsect1>
220 <refsect1>
221 <title>AUTHOR</title>
222 <para>This manual page was quickly copied from the glimmer web site by &dhusername; &dhemail; for
223 the &debian; system.
224 </para>
225 </refsect1>
226 </refentry>
227
228 <!-- Keep this comment at the end of the file
229 Local variables:
230 mode: sgml
231 sgml-omittag:t
232 sgml-shorttag:t
233 sgml-minimize-attributes:nil
234 sgml-always-quote-attributes:t
235 sgml-indent-step:2
236 sgml-indent-data:t
237 sgml-parent-document:nil
238 sgml-default-dtd-file:nil
239 sgml-exposed-tags:nil
240 sgml-local-catalogs:nil
241 sgml-local-ecat-files:nil
242 End:
243 -->
244
245
191191 <refsect1>
192192 <title>SEE ALSO</title>
193193 <para>
194 tigr-glimmer2 (1),
194 tigr-glimmer3 (1),
195195 tigr-adjust (1),
196196 tigr-anomaly (1),
197197 tigr-build-icm (1),
207207 http://www.tigr.org/software/glimmer/
208208 </para>
209209
210 <para>Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer2.</para>
210 <para>Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer3.</para>
211211 </refsect1>
212212 <refsect1>
213213 <title>AUTHOR</title>
+0
-120
debian/tigr-run-glimmer2.sgml less more
0 <!doctype refentry PUBLIC "-//OASIS//DTD DocBook V4.1//EN" [
1
2 <!-- Process this file with docbook-to-man to generate an nroff manual
3 page: `docbook-to-man manpage.sgml > manpage.1'. You may view
4 the manual page with: `docbook-to-man manpage.sgml | nroff -man |
5 less'. A typical entry in a Makefile or Makefile.am is:
6
7 manpage.1: manpage.sgml
8 docbook-to-man $< > $@
9
10
11 The docbook-to-man binary is found in the docbook-to-man package.
12 Please remember that if you create the nroff version in one of the
13 debian/rules file targets (such as build), you will need to include
14 docbook-to-man in your Build-Depends control field.
15
16 -->
17
18 <!-- Fill in your name for FIRSTNAME and SURNAME. -->
19 <!ENTITY dhfirstname "<firstname>Steffen</firstname>">
20 <!ENTITY dhsurname "<surname>Möller</surname>">
21 <!-- Please adjust the date whenever revising the manpage. -->
22 <!ENTITY dhdate "<date>November 10, 2004</date>">
23 <!ENTITY dhsection "<manvolnum>1</manvolnum>">
24 <!ENTITY dhemail "<email>moeller@pzr.uni-rostock.de</email>">
25 <!ENTITY dhusername "Steffen Moeller">
26 <!ENTITY dhucpackage "<refentrytitle>TIGR-GLIMMER</refentrytitle>">
27 <!ENTITY dhpackage "tigr-glimmer">
28
29 <!ENTITY debian "<productname>Debian</productname>">
30 <!ENTITY gnu "<acronym>GNU</acronym>">
31 <!ENTITY gpl "&gnu; <acronym>GPL</acronym>">
32 ]>
33
34 <refentry>
35 <refentryinfo>
36 <address>
37 &dhemail;
38 </address>
39 <author>
40 &dhfirstname;
41 &dhsurname;
42 </author>
43 <copyright>
44 <year>2003</year>
45 <holder>&dhusername;</holder>
46 </copyright>
47 &dhdate;
48 </refentryinfo>
49 <refmeta>
50 &dhucpackage;
51
52 &dhsection;
53 </refmeta>
54 <refnamediv>
55 <refname>&dhpackage;</refname>
56
57 <refpurpose>
58 Apply the suite of programs within glimmer2 to a a prokaryotic or archean genome.
59 </refpurpose>
60 </refnamediv>
61 <refsynopsisdiv>
62 <cmdsynopsis>
63 <command>tigr-run-glimmer2</command>
64 </cmdsynopsis>
65 </refsynopsisdiv>
66 <refsect1>
67 <title>DESCRIPTION</title>
68 <para>
69 A shell script that wraps a set of tigr-* utilities of the glimmer package to retrieve coding regions.
70 </para>
71 </refsect1>
72 <refsect1>
73 <title>SEE ALSO</title>
74 <para>
75 tigr-glimmer2 (1),
76 tigr-adjust (1),
77 tigr-anomaly (1),
78 tigr-build-icm (1),
79 tigr-check (1),
80 tigr-codon-usage (1),
81 tigr-compare-lists (1),
82 tigr-extract (1),
83 tigr-generate (1),
84 tigr-get-len (1),
85 tigr-get-putative (1),
86 tigr-long-orfs (1),
87 </para>
88 <para>
89 http://www.tigr.org/software/glimmer/
90 </para>
91
92 <para>Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer2.</para>
93 </refsect1>
94 <refsect1>
95 <title>AUTHOR</title>
96
97 <para>This manual page was quickly copied from the glimmer web site by &dhusername; &dhemail; for
98 the &debian; system.
99 </para>
100
101 </refsect1>
102 </refentry>
103
104 <!-- Keep this comment at the end of the file
105 Local variables:
106 mode: sgml
107 sgml-omittag:t
108 sgml-shorttag:t
109 sgml-minimize-attributes:nil
110 sgml-always-quote-attributes:t
111 sgml-indent-step:2
112 sgml-indent-data:t
113 sgml-parent-document:nil
114 sgml-default-dtd-file:nil
115 sgml-exposed-tags:nil
116 sgml-local-catalogs:nil
117 sgml-local-ecat-files:nil
118 End:
119 -->
0 <!doctype refentry PUBLIC "-//OASIS//DTD DocBook V4.1//EN" [
1
2 <!-- Process this file with docbook-to-man to generate an nroff manual
3 page: `docbook-to-man manpage.sgml > manpage.1'. You may view
4 the manual page with: `docbook-to-man manpage.sgml | nroff -man |
5 less'. A typical entry in a Makefile or Makefile.am is:
6
7 manpage.1: manpage.sgml
8 docbook-to-man $< > $@
9
10
11 The docbook-to-man binary is found in the docbook-to-man package.
12 Please remember that if you create the nroff version in one of the
13 debian/rules file targets (such as build), you will need to include
14 docbook-to-man in your Build-Depends control field.
15
16 -->
17
18 <!-- Fill in your name for FIRSTNAME and SURNAME. -->
19 <!ENTITY dhfirstname "<firstname>Steffen</firstname>">
20 <!ENTITY dhsurname "<surname>Möller</surname>">
21 <!-- Please adjust the date whenever revising the manpage. -->
22 <!ENTITY dhdate "<date>November 10, 2004</date>">
23 <!ENTITY dhsection "<manvolnum>1</manvolnum>">
24 <!ENTITY dhemail "<email>moeller@pzr.uni-rostock.de</email>">
25 <!ENTITY dhusername "Steffen Moeller">
26 <!ENTITY dhucpackage "<refentrytitle>TIGR-GLIMMER</refentrytitle>">
27 <!ENTITY dhpackage "tigr-glimmer">
28
29 <!ENTITY debian "<productname>Debian</productname>">
30 <!ENTITY gnu "<acronym>GNU</acronym>">
31 <!ENTITY gpl "&gnu; <acronym>GPL</acronym>">
32 ]>
33
34 <refentry>
35 <refentryinfo>
36 <address>
37 &dhemail;
38 </address>
39 <author>
40 &dhfirstname;
41 &dhsurname;
42 </author>
43 <copyright>
44 <year>2003</year>
45 <holder>&dhusername;</holder>
46 </copyright>
47 &dhdate;
48 </refentryinfo>
49 <refmeta>
50 &dhucpackage;
51
52 &dhsection;
53 </refmeta>
54 <refnamediv>
55 <refname>&dhpackage;</refname>
56
57 <refpurpose>
58 Apply the suite of programs within glimmer3 to a a prokaryotic or archean genome.
59 </refpurpose>
60 </refnamediv>
61 <refsynopsisdiv>
62 <cmdsynopsis>
63 <command>tigr-run-glimmer3</command>
64 </cmdsynopsis>
65 </refsynopsisdiv>
66 <refsect1>
67 <title>DESCRIPTION</title>
68 <para>
69 A shell script that wraps a set of tigr-* utilities of the glimmer package to retrieve coding regions.
70 </para>
71 </refsect1>
72 <refsect1>
73 <title>SEE ALSO</title>
74 <para>
75 tigr-glimmer3 (1),
76 tigr-adjust (1),
77 tigr-anomaly (1),
78 tigr-build-icm (1),
79 tigr-check (1),
80 tigr-codon-usage (1),
81 tigr-compare-lists (1),
82 tigr-extract (1),
83 tigr-generate (1),
84 tigr-get-len (1),
85 tigr-get-putative (1),
86 tigr-long-orfs (1),
87 </para>
88 <para>
89 http://www.tigr.org/software/glimmer/
90 </para>
91
92 <para>Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer3.</para>
93 </refsect1>
94 <refsect1>
95 <title>AUTHOR</title>
96
97 <para>This manual page was quickly copied from the glimmer web site by &dhusername; &dhemail; for
98 the &debian; system.
99 </para>
100
101 </refsect1>
102 </refentry>
103
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118 End:
119 -->