Package list tigr-glimmer / b35cc01
Do not use docbook-to-man to create manpages Andreas Tille 1 year, 7 months ago
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0 tigr-glimmer (3.02b-3) UNRELEASED; urgency=medium
0 tigr-glimmer (3.02b-3) unstable; urgency=medium
11
22 [ Steffen Möller ]
33 * Updated d/u/metadata
1414 * Trim trailing whitespace.
1515 * Wrap long lines in changelog entries: 2.13-1.
1616 * Refer to specific version of license GPL-2+.
17 * Do not use docbook-to-man to create manpages
1718
18 -- Andreas Tille <tille@debian.org> Wed, 29 Apr 2020 22:52:39 +0200
19 -- Andreas Tille <tille@debian.org> Wed, 29 Apr 2020 22:53:42 +0200
1920
2021 tigr-glimmer (3.02b-2) unstable; urgency=medium
2122
33 Andreas Tille <tille@debian.org>
44 Section: science
55 Priority: optional
6 Build-Depends: debhelper-compat (= 12),
7 docbook-to-man
6 Build-Depends: debhelper-compat (= 12)
87 Standards-Version: 4.5.0
98 Vcs-Browser: https://salsa.debian.org/med-team/tigr-glimmer
109 Vcs-Git: https://salsa.debian.org/med-team/tigr-glimmer.git
0 .TH "TIGR-GLIMMER" "1"
1 .SH "NAME"
2 tigr-glimmer \(em The program lacks a description
3 .SH "SYNOPSIS"
4 .PP
5 \fBtigr-anomaly\fR [>dna-file] [>coord-file]
6 .SH "DESCRIPTION"
7 .PP
8 .SH "OPTIONS"
9 .SH "SEE ALSO"
10 .PP
11 tigr-glimmer3 (1),
12 tigr-adjust (1),
13 tigr-anomaly (1),
14 tigr-build-icm (1),
15 tigr-check (1),
16 tigr-codon-usage (1),
17 tigr-compare-lists (1),
18 tigr-extract (1),
19 tigr-generate (1),
20 tigr-get-len (1),
21 tigr-get-putative (1),
22 .PP
23 http://www.tigr.org/software/glimmer/
24 .PP
25 Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer3.
26 .SH "AUTHOR"
27 .PP
28 This manual page was quickly copied from the glimmer web site by Steffen Moeller moeller@debian.org for
29 the \fBDebian\fP system.
30
31 .\" created by instant / docbook-to-man
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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@debian.org</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 The program lacks a description
59 </refpurpose>
60 </refnamediv>
61 <refsynopsisdiv>
62 <cmdsynopsis>
63 <command>tigr-anomaly</command>
64 <arg>>dna-file</arg>
65 <arg>>coord-file</arg>
66 </cmdsynopsis>
67 </refsynopsisdiv>
68 <refsect1>
69 <title>DESCRIPTION</title>
70 <para>
71 </para>
72
73 </refsect1>
74 <refsect1>
75 <title>OPTIONS</title>
76 </refsect1>
77 <refsect1>
78 <title>SEE ALSO</title>
79 <para>
80 tigr-glimmer3 (1),
81 tigr-adjust (1),
82 tigr-anomaly (1),
83 tigr-build-icm (1),
84 tigr-check (1),
85 tigr-codon-usage (1),
86 tigr-compare-lists (1),
87 tigr-extract (1),
88 tigr-generate (1),
89 tigr-get-len (1),
90 tigr-get-putative (1),
91 </para>
92 <para>
93 http://www.tigr.org/software/glimmer/
94 </para>
95
96 <para>Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer3.</para>
97 </refsect1>
98 <refsect1>
99 <title>AUTHOR</title>
100
101 <para>This manual page was quickly copied from the glimmer web site by &dhusername; &dhemail; for
102 the &debian; system.
103 </para>
104
105 </refsect1>
106 </refentry>
107
108 <!-- Keep this comment at the end of the file
109 Local variables:
110 mode: sgml
111 sgml-omittag:t
112 sgml-shorttag:t
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0 .TH "TIGR-GLIMMER \fB(1)\fP " "1"
1 .SH "NAME"
2 tigr-glimmer \(em Creates and outputs an interpolated Markov model(IMM)
3 .SH "SYNOPSIS"
4 .PP
5 \fBtigr-build-icm\fR
6 .SH "DESCRIPTION"
7 .PP
8 Program build-icm.c creates and outputs an interpolated Markov
9 model (IMM) as described in the paper
10 A.L. Delcher, D. Harmon, S. Kasif, O. White, and S.L. Salzberg.
11 Improved Microbial Gene Identification with Glimmer.
12 Nucleic Acids Research, 1999, in press.
13 Please reference this paper if you use the system as part of any
14 published research.
15 .PP
16 Input comes from the file named on the command-line. Format should be
17 one string per line. Each line has an ID string followed by white space
18 followed by the sequence itself. The script run-glimmer3 generates
19 an input file in the correct format using the 'extract' program.
20 .PP
21 The IMM is constructed as follows: For a given context, say
22 acgtta, we want to estimate the probability distribution of the
23 next character. We shall do this as a linear combination of the
24 observed probability distributions for this context and all of
25 its suffixes, i.e., cgtta, gtta, tta, ta, a and empty. By
26 observed distributions I mean the counts of the number of
27 occurrences of these strings in the training set. The linear
28 combination is determined by a set of probabilities, lambda, one
29 for each context string. For context acgtta the linear combination
30 coefficients are:
31 .PP
32 lambda (acgtta)
33 (1 \- lambda (acgtta)) x lambda (cgtta)
34 (1 \- lambda (acgtta)) x (1 \- lambda (cgtta)) x lambda (gtta)
35 (1 \- lambda (acgtta)) x (1 \- lambda (cgtta)) x (1 \- lambda (gtta)) x lambda (tta)
36 (1 \- lambda (acgtta)) x (1 \- lambda (cgtta)) x (1 \- lambda (gtta))
37 x (1 \- lambda (tta)) x (1 \- lambda (ta)) x (1 \- lambda (a))
38 .PP
39 We compute the lambda values for each context as follows:
40 \- If the number of observations in the training set is >= the constant
41 SAMPLE_SIZE_BOUND, the lambda for that context is 1.0
42 \- Otherwise, do a chi-square test on the observations for this context
43 compared to the distribution predicted for the one-character shorter
44 suffix context.
45 If the chi-square significance < 0.5, set the lambda for this context to 0.0
46 Otherwise set the lambda for this context to:
47 (chi-square significance) x (# observations) / SAMPLE_WEIGHT
48 .PP
49 To run the program:
50 .PP
51 build-icm <train.seq > train.model
52 .PP
53 This will use the training data in train.seq to produce the file
54 train.model, containing your IMM.
55 .SH "SEE ALSO"
56 .PP
57 tigr-glimmer3 (1),
58 tigr-long-orfs (1),
59 tigr-adjust (1),
60 tigr-anomaly (1),
61 tigr-extract (1),
62 tigr-check (1),
63 tigr-codon-usage (1),
64 tigr-compare-lists (1),
65 tigr-extract (1),
66 tigr-generate (1),
67 tigr-get-len (1),
68 tigr-get-putative (1),
69
70 .PP
71 http://www.tigr.org/software/glimmer/
72 .PP
73 Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer3.
74 .SH "AUTHOR"
75 .PP
76 This manual page was quickly copied from the glimmer web site and readme file by Steffen Moeller moeller@debian.org for
77 the \fBDebian\fP system.
78
79 .\" created by instant / docbook-to-man
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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>Novemver 10, 2004</date>">
23 <!ENTITY dhsection "<manvolnum>1</manvolnum>">
24 <!ENTITY dhemail "<email>moeller@debian.org</email>">
25 <!ENTITY dhusername "Steffen Moeller">
26 <!ENTITY dhucpackage "<refentrytitle>TIGR-GLIMMER<title>">
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>Creates and outputs an interpolated Markov model(IMM)</refpurpose>
57 </refnamediv>
58 <refsynopsisdiv>
59 <cmdsynopsis>
60 <command>tigr-build-icm</command>
61 </cmdsynopsis>
62 </refsynopsisdiv>
63 <refsect1>
64 <title>DESCRIPTION</title>
65 <para>
66 Program build-icm.c creates and outputs an interpolated Markov
67 model (IMM) as described in the paper
68 A.L. Delcher, D. Harmon, S. Kasif, O. White, and S.L. Salzberg.
69 Improved Microbial Gene Identification with Glimmer.
70 Nucleic Acids Research, 1999, in press.
71 Please reference this paper if you use the system as part of any
72 published research.
73 </para><para>
74 Input comes from the file named on the command-line. Format should be
75 one string per line. Each line has an ID string followed by white space
76 followed by the sequence itself. The script run-glimmer3 generates
77 an input file in the correct format using the 'extract' program.
78 </para><para>
79 The IMM is constructed as follows: For a given context, say
80 acgtta, we want to estimate the probability distribution of the
81 next character. We shall do this as a linear combination of the
82 observed probability distributions for this context and all of
83 its suffixes, i.e., cgtta, gtta, tta, ta, a and empty. By
84 observed distributions I mean the counts of the number of
85 occurrences of these strings in the training set. The linear
86 combination is determined by a set of probabilities, lambda, one
87 for each context string. For context acgtta the linear combination
88 coefficients are:
89 </para><para>
90 lambda (acgtta)
91 (1 - lambda (acgtta)) x lambda (cgtta)
92 (1 - lambda (acgtta)) x (1 - lambda (cgtta)) x lambda (gtta)
93 (1 - lambda (acgtta)) x (1 - lambda (cgtta)) x (1 - lambda (gtta)) x lambda (tta)
94 (1 - lambda (acgtta)) x (1 - lambda (cgtta)) x (1 - lambda (gtta))
95 x (1 - lambda (tta)) x (1 - lambda (ta)) x (1 - lambda (a))
96 </para><para>
97 We compute the lambda values for each context as follows:
98 - If the number of observations in the training set is &gt;= the constant
99 SAMPLE_SIZE_BOUND, the lambda for that context is 1.0
100 - Otherwise, do a chi-square test on the observations for this context
101 compared to the distribution predicted for the one-character shorter
102 suffix context.
103 If the chi-square significance &lt; 0.5, set the lambda for this context to 0.0
104 Otherwise set the lambda for this context to:
105 (chi-square significance) x (# observations) / SAMPLE_WEIGHT
106 </para><para>
107 To run the program:
108 </para><para>
109 build-icm &lt;train.seq &gt; train.model
110 </para><para>
111 This will use the training data in train.seq to produce the file
112 train.model, containing your IMM.
113 </para>
114 </refsect1>
115 <refsect1>
116 <title>SEE ALSO</title>
117 <para>
118 tigr-glimmer3 (1),
119 tigr-long-orfs (1),
120 tigr-adjust (1),
121 tigr-anomaly (1),
122 tigr-extract (1),
123 tigr-check (1),
124 tigr-codon-usage (1),
125 tigr-compare-lists (1),
126 tigr-extract (1),
127 tigr-generate (1),
128 tigr-get-len (1),
129 tigr-get-putative (1),
130 </para>
131 <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 Glimmer3.</para>
133 </refsect1>
134 <refsect1>
135 <title>AUTHOR</title>
136
137 <para>This manual page was quickly copied from the glimmer web site and readme file by &dhusername; &dhemail; for
138 the &debian; system.
139 </para>
140
141 </refsect1>
142 </refentry>
143
144 <!-- Keep this comment at the end of the file
145 Local variables:
146 mode: sgml
147 sgml-omittag:t
148 sgml-shorttag:t
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155 sgml-exposed-tags:nil
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157 sgml-local-ecat-files:nil
158 End:
159 -->
160
161
0 .TH "TIGR-GLIMMER" "1"
1 .SH "NAME"
2 tigr-glimmer \(em Fine start/stop positions of genes in genome sequence
3 .SH "SYNOPSIS"
4 .PP
5 \fBtigr-extract\fR [genome-file \fB\fIoptions\fR\fP]
6 .SH "DESCRIPTION"
7 .PP
8 Program extract takes a FASTA format sequence file and a file
9 with a list of start/stop positions in that file (e.g., as produced
10 by the long-orfs program) and extracts and outputs the
11 specified sequences.
12 .PP
13 The first command-line argument is the name of the sequence file,
14 which must be in FASTA format.
15 .PP
16 The second command-line argument is the name of the coordinate file.
17 It must contain a list of pairs of positions in the first file, one
18 per line. The format of each entry is:
19 .PP
20 <IDstring>> <start position> <stop position>
21 .PP
22 This file should contain no other information, so if you're using
23 the output of glimmer or long-orfs , you'll have to cut off
24 header lines.
25 .PP
26 The output of the program goes to the standard output and has one
27 line for each line in the coordinate file. Each line contains
28 the IDstring , followed by white space, followed by the substring
29 of the sequence file specified by the coordinate pair. Specifically,
30 the substring starts at the first position of the pair and ends at
31 the second position (inclusive). If the first position is bigger
32 than the second, then the DNA reverse complement of each position
33 is generated. Start/stop pairs that "wrap around" the end of the
34 genome are allowed.
35 .SH "OPTIONS"
36 .IP "\fB-skip\fP" 10
37 makes the output omit the first 3 characters of each sequence, i.e., it skips over the start codon. This was the behaviour of the previous version of the program.
38 .IP "\fB-l\fP" 10
39 makes the output omit an sequences shorter than n characters.
40 n includes the 3 skipped characters if the \-skip switch
41 is one.
42
43 .SH "SEE ALSO"
44 .PP
45 tigr-glimmer3 (1),
46 tigr-long-orfs (1),
47 tigr-adjust (1),
48 tigr-anomaly (1),
49 tigr-build-icm (1),
50 tigr-check (1),
51 tigr-codon-usage (1),
52 tigr-compare-lists (1),
53 tigr-extract (1),
54 tigr-generate (1),
55 tigr-get-len (1),
56 tigr-get-putative (1),
57 .PP
58 http://www.tigr.org/software/glimmer/
59 .PP
60 Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer3.
61 .SH "AUTHOR"
62 .PP
63 This manual page was quickly copied from the glimmer web site by Steffen Moeller moeller@debian.org for
64 the \fBDebian\fP system.
65
66 .\" created by instant / docbook-to-man
+0
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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@debian.org</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 Fine start/stop positions of genes in genome sequence
59 </refpurpose>
60 </refnamediv>
61 <refsynopsisdiv>
62 <cmdsynopsis>
63 <command>tigr-extract</command>
64 <arg>genome-file <option><replaceable>options</replaceable></option></arg>
65 </cmdsynopsis>
66 </refsynopsisdiv>
67 <refsect1>
68 <title>DESCRIPTION</title>
69 <para>
70 Program extract takes a FASTA format sequence file and a file
71 with a list of start/stop positions in that file (e.g., as produced
72 by the long-orfs program) and extracts and outputs the
73 specified sequences.
74 </para><para>
75 The first command-line argument is the name of the sequence file,
76 which must be in FASTA format.
77 </para><para>
78 The second command-line argument is the name of the coordinate file.
79 It must contain a list of pairs of positions in the first file, one
80 per line. The format of each entry is:
81 </para><para> &lt;IDstring>&gt; &lt;start position> &lt;stop position&gt;
82 </para><para>This file should contain no other information, so if you're using
83 the output of glimmer or long-orfs , you'll have to cut off
84 header lines.
85 </para><para>
86 The output of the program goes to the standard output and has one
87 line for each line in the coordinate file. Each line contains
88 the IDstring , followed by white space, followed by the substring
89 of the sequence file specified by the coordinate pair. Specifically,
90 the substring starts at the first position of the pair and ends at
91 the second position (inclusive). If the first position is bigger
92 than the second, then the DNA reverse complement of each position
93 is generated. Start/stop pairs that "wrap around" the end of the
94 genome are allowed.
95 </para>
96 </refsect1>
97 <refsect1>
98 <title>OPTIONS</title>
99 <variablelist>
100 <varlistentry>
101 <term><option>-skip</option></term>
102 <listitem>
103 <para> makes the output omit the first 3 characters of each sequence, i.e., it skips over the start codon. This was the behaviour of the previous version of the program.</para>
104 </listitem>
105 </varlistentry>
106 <varlistentry>
107 <term><option>-l</option></term><listitem><para>
108 makes the output omit an sequences shorter than n characters.
109 n includes the 3 skipped characters if the -skip switch
110 is one.
111 </para></listitem>
112 </varlistentry>
113 </variablelist>
114 </refsect1>
115 <refsect1>
116 <title>SEE ALSO</title>
117 <para>
118 tigr-glimmer3 (1),
119 tigr-long-orfs (1),
120 tigr-adjust (1),
121 tigr-anomaly (1),
122 tigr-build-icm (1),
123 tigr-check (1),
124 tigr-codon-usage (1),
125 tigr-compare-lists (1),
126 tigr-extract (1),
127 tigr-generate (1),
128 tigr-get-len (1),
129 tigr-get-putative (1),
130 </para>
131 <para>
132 http://www.tigr.org/software/glimmer/
133 </para>
134
135 <para>Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer3.</para>
136 </refsect1>
137 <refsect1>
138 <title>AUTHOR</title>
139
140 <para>This manual page was quickly copied from the glimmer web site by &dhusername; &dhemail; for
141 the &debian; system.
142 </para>
143
144 </refsect1>
145 </refentry>
146
147 <!-- Keep this comment at the end of the file
148 Local variables:
149 mode: sgml
150 sgml-omittag:t
151 sgml-shorttag:t
152 sgml-minimize-attributes:nil
153 sgml-always-quote-attributes:t
154 sgml-indent-step:2
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158 sgml-exposed-tags:nil
159 sgml-local-catalogs:nil
160 sgml-local-ecat-files:nil
161 End:
162 -->
163
164
0 .TH TIGR-GLIMMER 1 "April 16, 2008"
1 .SH NAME
2 tigr-glimmer \- runs various programs of the TIGR Glimmer suite
3 .SH SYNOPSIS
4 .B tigr-glimmer
5 .B program
6 [arguments]
7 .SH DESCRIPTION
8 This manual page documents briefly the
9 .B tigr-glimmer
10 wrapper to the TIGR Glimmer programs.
11 This manual page was written for the Debian GNU/Linux distribution
12 because upstream does not provide this wrapper and it was invented
13 for Debian to avoid conflicts with other packages that might cause
14 a name space pollution.
15 .PP
16 \fBtigr-glimmer\fP is just a wrapper that invokes the various programs in
17 the TIGR Glimmer software package. You can get more detailed documentation
18 in /usr/share/doc/tigr-glimmer. Please note that the documentation there
19 is a part of the former version Glimmer 2. The version Glimmer 3 has
20 some features that were described in the notes.pdf document inside
21 the documentation directory.
22 .PP
23 The following programs are included: anomaly, build-fixed, build-icm,
24 entropy-profile, entropy-score, extract, glimmer3, long-orfs, multi-extract,
25 score-fixed, start-codon-distrib, test, uncovered and window-acgt.
26 .SH OPTIONS
27 There are no options.
28 .SH EXAMPLES
29 .IP tigr-glimmer\ build-icm
30 .IP tigr-glimmer\ long-orfs
31 .SH SEE ALSO
32 For the pre previously packaged version Glimmer2 some text files from
33 the documentation were turned to man pages for the Debian GNU/Linux
34 distribution by Steffen Moeller <moeller@debian.org>
35 .br
36 .SH AUTHORS
37 This manual page was written by Andreas Tille <tille@debian.org>, for
38 the Debian GNU/Linux system (but may be used by others).
0 .TH "TIGR-GLIMMER" "1"
1 .SH "NAME"
2 tigr-glimmer \(em Find/Score potential genes in genome-file using the probability model in icm-file
3 .SH "SYNOPSIS"
4 .PP
5 \fBtigr-glimmer3\fR [\fB\fIgenome-file\fR\fP] [\fB\fIicm-file\fR\fP] [\fB\fI[options]\fR\fP]
6 .SH "DESCRIPTION"
7 .PP
8 \fBtigr-glimmer\fR is a system for finding genes in microbial DNA, especially the genomes of bacteria and archaea. \fBtigr-glimmer\fR (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 \fBtigr-glimmer\fR 1.0 and in our subsequent paper on \fBtigr-glimmer\fR 2.0, uses a combination of Markov models from 1st through 8th-order, weighting each model according to its predictive power. \fBtigr-glimmer\fR 1.0 and 2.0 use 3-periodic nonhomogenous Markov models in their IMMs.
9 .PP
10 \fBtigr-glimmer\fR 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.
11 .PP
12 A special version of \fBtigr-glimmer\fR 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.
13 .PP
14 The \fBtigr-glimmer\fR 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. \fBtigr-glimmer\fR 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.
15 \fBtigr-glimmer\fR is a program that...
16 .SH "OPTIONS"
17 .IP "\fB-C \fIn\fR\fP" 10
18 Use n as GC percentage of independent model
19 .IP "" 10
20 Note: n should be a percentage, e.g., \-C 45.2
21 .IP "\-f" 10
22 Use ribosome-binding energy to choose start codon
23 .IP "\fB+f\fP" 10
24 Use first codon in orf as start codon
25 .IP "\fB-g \fIn\fR\fP" 10
26 Set minimum gene length to n
27 .IP "\fB-i \fIfilename\fR\fP" 10
28 Use \fB\fIfilename\fR\fP to select regions of bases that are off
29 limits, so that no bases within that area will be examined
30
31 .IP "\fB-l\fP" 10
32 Assume linear rather than circular genome, i.e., no wraparound
33 .IP "\fB-L \fIfilename\fR\fP" 10
34 Use filename to specify a list of orfs that should
35 be scored separately, with no overlap rules
36
37 .IP "\fB-M\fP" 10
38 Input is a multifasta file of separate genes to be scored
39 separately, with no overlap rules
40
41 .IP "\fB-o \fIn\fR\fP" 10
42 Set minimum overlap length to n. Overlaps shorter than this
43 are ignored.
44
45 .IP "\fB-p \fIn\fR\fP" 10
46 Set minimum overlap percentage to n%. Overlaps shorter than this percentage of *both* strings are ignored.
47
48 .IP "\fB-q \fIn\fR\fP" 10
49 Set the maximum length orf that can be rejected because of
50 the independent probability score column to (n \- 1)
51
52 .IP "\fB-r\fP" 10
53 Don't use independent probability score column
54
55 .IP "\fB+r\fP" 10
56 Use independent probability score column
57
58 .IP "\fB-r\fP" 10
59 Don't use independent probability score column
60
61 .IP "\fB-s \fIs\fR\fP" 10
62 Use string s as the ribosome binding pattern to find start codons.
63 .IP "\fB+S\fP" 10
64 Do use stricter independent intergenic model that doesn't
65 give probabilities to in-frame stop codons. (Option is obsolete
66 since this is now the only behaviour
67
68 .IP "\fB-t \fIn\fR\fP" 10
69 Set threshold score for calling as gene to n. If the in-frame
70 score >= n, then the region is given a number and considered
71 a potential gene.
72
73 .IP "\fB-w \fIn\fR \fP" 10
74 Use "weak" scores on tentative genes n or longer. Weak
75 scores ignore the independent probability score.
76
77 .SH "SEE ALSO"
78 .PP
79 tigr-adjust (1),
80 tigr-anomaly (1),
81 tigr-build-icm (1),
82 tigr-check (1),
83 tigr-codon-usage (1),
84 tigr-compare-lists (1),
85 tigr-extract (1),
86 tigr-generate (1),
87 tigr-get-len (1),
88 tigr-get-putative (1),
89 tigr-glimmer3 (1),
90 tigr-long-orfs (1)
91 .PP
92 http://www.tigr.org/software/glimmer/
93 .PP
94 Please see the readme in /usr/share/doc/glimmer for a description on how to use Glimmer.
95 .SH "AUTHOR"
96 .PP
97 This manual page was quickly copied from the glimmer web site by Steffen Moeller moeller@debian.org for
98 the \fBDebian\fP system.
99
100 .\" created by instant / docbook-to-man
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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@debian.org</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
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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 .TH "LONG-ORFS" "1"
1 .SH "NAME"
2 long-orfs \(em Find/Score potential genes in genome-file using
3 the probability model in icm-file
4 .SH "SYNOPSIS"
5 .PP
6 \fBtigr-long-orgs\fR [genome-file \fB\fIoptions\fR\fP]
7 .SH "DESCRIPTION"
8 .PP
9 Program long-orfs takes a sequence file (in FASTA format) and
10 outputs a list of all long "potential genes" in it that do not
11 overlap by too much. By "potential gene" I mean the portion of
12 an orf from the first start codon to the stop codon at the end.
13 .PP
14 The first few lines of output specify the settings of various
15 parameters in the program:
16 .PP
17 Minimum gene length is the length of the smallest fragment
18 considered to be a gene. The length is measured from the first base
19 of the start codon to the last base *before* the stop codon.
20 This value can be specified when running the program with the \-g option.
21 By default, the program now (April 2003) will compute an optimal length
22 for this parameter, where "optimal" is the value that produces the
23 greatest number of long ORFs, thereby increasing the amount of data
24 used for training.
25 .PP
26 Minimum overlap length is a lower bound on the number of bases overlap
27 between 2 genes that is considered a problem. Overlaps shorter than
28 this are ignored.
29 .PP
30 Minimum overlap percent is another lower bound on the number of bases
31 overlap that is considered a problem. Overlaps shorter than this
32 percentage of *both* genes are ignored.
33 .PP
34 The next portion of the output is a list of potential genes:
35 .PP
36 Column 1 is an ID number for reference purposes. It is assigned
37 sequentially starting with 1 to all long potential genes. If
38 overlapping genes are eliminated, gaps in the numbers will occur.
39 The ID prefix is specified in the constant ID_PREFIX .
40 .PP
41 Column 2 is the position of the first base of the first start codon in
42 the orf. Currently I use atg, and gtg as start codons. This is
43 easily changed in the function Is_Start () .
44 .PP
45 Column 3 is the position of the last base *before* the stop codon. Stop
46 codons are taa, tag, and tga. Note that for orfs in the reverse
47 reading frames have their start position higher than the end position.
48 The order in which orfs are listed is in increasing order by
49 Max {OrfStart, End}, i.e., the highest numbered position in the orf,
50 except for orfs that "wrap around" the end of the sequence.
51 .PP
52 When two genes with ID numbers overlap by at least a sufficient
53 amount (as determined by Min_Olap and Min_Olap_Percent ), they
54 are eliminated and do not appear in the output.
55 .PP
56 The final output of the program (sent to the standard error file so
57 it does not show up when output is redirected to a file) is the
58 length of the longest orf found.
59 .PP
60
61 Specifying Different Start and Stop Codons:
62 .PP
63 To specify different sets of start and stop codons, modify the file
64 gene.h . Specifically, the functions:
65 .PP
66 Is_Forward_Start Is_Reverse_Start Is_Start
67 Is_Forward_Stop Is_Reverse_Stop Is_Stop
68 .PP
69 are used to determine what is used for start and stop codons.
70 .PP
71 Is_Start and Is_Stop do simple string comparisons to specify
72 which patterns are used. To add a new pattern, just add the comparison
73 for it. To remove a pattern, comment out or delete the comparison
74 for it.
75 .PP
76 The other four functions use a bit comparison to determine start and
77 stop patterns. They represent a codon as a 12-bit pattern, with 4 bits
78 for each base, one bit for each possible value of the bases, T, G, C
79 or A. Thus the bit pattern 0010 0101 1100 represents the base
80 pattern [C] [A or G] [G or T]. By doing bit operations (& | ~) and
81 comparisons, more complicated patterns involving ambiguous reads
82 can be tested efficiently. Simple patterns can be tested as in
83 the current code.
84 .PP
85 For example, to insert an additional start codon of CAT requires 3 changes:
86 1. The line
87 || (Codon & 0x218) == Codon
88 should be inserted into Is_Forward_Start , since 0x218 = 0010 0001 1000
89 represents CAT.
90 2. The line
91 || (Codon & 0x184) == Codon
92 should be inserted into Is_Reverse_Start , since 0x184 = 0001 1000 0100
93 represents ATG, which is the reverse-complement of CAT. Alternately,
94 the #define constant ATG_MASK could be used.
95 3. The line
96 || strncmp (S, "cat", 3) == 0
97 should be inserted into Is_Start .
98 .SH "OPTIONS"
99 .IP "\fB-g \fIn\fR\fP" 10
100 Set minimum gene length to n. Default is to compute an
101 optimal value automatically. Don't change this unless you
102 know what you're doing.
103 .IP "\fB-l\fP" 10
104 Regard the genome as linear (not circular), i.e., do not allow
105 genes to "wrap around" the end of the genome.
106 This option works on both glimmer and long-orfs .
107 The default behavior is to regard the genome as circular.
108 .IP "\fB-o \fIn\fR\fP" 10
109 Set maximum overlap length to n. Overlaps shorter than this
110 are permitted. (Default is 0 bp.)
111 .IP "\fB-p \fIn\fR\fP" 10
112 Set maximum overlap percentage to n%. Overlaps shorter than
113 this percentage of *both* strings are ignored. (Default is 10%.)
114 .SH "SEE ALSO"
115 .PP
116 tigr-glimmer3 (1),
117 tigr-adjust (1),
118 tigr-anomaly (1),
119 tigr-build-icm (1),
120 tigr-check (1),
121 tigr-codon-usage (1),
122 tigr-compare-lists (1),
123 tigr-extract (1),
124 tigr-generate (1),
125 tigr-get-len (1),
126 tigr-get-putative (1),
127 .PP
128 http://www.tigr.org/software/glimmer/
129 .PP
130 Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer3.
131 .SH "AUTHOR"
132 .PP
133 This manual page was quickly copied from the glimmer web site by Steffen Moeller moeller@debian.org for
134 the \fBDebian\fP system.
135
136 .\" created by instant / docbook-to-man
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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@debian.org</email>">
25 <!ENTITY dhusername "Steffen Moeller">
26 <!ENTITY dhucpackage "<refentrytitle>LONG-ORFS</refentrytitle>">
27 <!ENTITY dhpackage "long-orfs">
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 Find/Score potential genes in genome-file using
59 the probability model in icm-file
60 </refpurpose>
61 </refnamediv>
62 <refsynopsisdiv>
63 <cmdsynopsis>
64 <command>tigr-long-orgs</command>
65 <arg>genome-file <option><replaceable>options</replaceable></option></arg>
66 </cmdsynopsis>
67 </refsynopsisdiv>
68 <refsect1>
69 <title>DESCRIPTION</title>
70 <para>
71 Program long-orfs takes a sequence file (in FASTA format) and
72 outputs a list of all long "potential genes" in it that do not
73 overlap by too much. By "potential gene" I mean the portion of
74 an orf from the first start codon to the stop codon at the end.
75 </para><para>
76 The first few lines of output specify the settings of various
77 parameters in the program:
78 </para><para>
79 Minimum gene length is the length of the smallest fragment
80 considered to be a gene. The length is measured from the first base
81 of the start codon to the last base *before* the stop codon.
82 This value can be specified when running the program with the -g option.
83 By default, the program now (April 2003) will compute an optimal length
84 for this parameter, where "optimal" is the value that produces the
85 greatest number of long ORFs, thereby increasing the amount of data
86 used for training.
87 </para><para>
88 Minimum overlap length is a lower bound on the number of bases overlap
89 between 2 genes that is considered a problem. Overlaps shorter than
90 this are ignored.
91 </para><para>
92 Minimum overlap percent is another lower bound on the number of bases
93 overlap that is considered a problem. Overlaps shorter than this
94 percentage of *both* genes are ignored.
95 </para><para>
96 The next portion of the output is a list of potential genes:
97 </para><para>
98 Column 1 is an ID number for reference purposes. It is assigned
99 sequentially starting with 1 to all long potential genes. If
100 overlapping genes are eliminated, gaps in the numbers will occur.
101 The ID prefix is specified in the constant ID_PREFIX .
102 </para><para>
103 Column 2 is the position of the first base of the first start codon in
104 the orf. Currently I use atg, and gtg as start codons. This is
105 easily changed in the function Is_Start () .
106 </para><para>
107 Column 3 is the position of the last base *before* the stop codon. Stop
108 codons are taa, tag, and tga. Note that for orfs in the reverse
109 reading frames have their start position higher than the end position.
110 The order in which orfs are listed is in increasing order by
111 Max {OrfStart, End}, i.e., the highest numbered position in the orf,
112 except for orfs that "wrap around" the end of the sequence.
113 </para><para>
114 When two genes with ID numbers overlap by at least a sufficient
115 amount (as determined by Min_Olap and Min_Olap_Percent ), they
116 are eliminated and do not appear in the output.
117 </para><para>
118 The final output of the program (sent to the standard error file so
119 it does not show up when output is redirected to a file) is the
120 length of the longest orf found.
121 </para><para>
122
123
124 Specifying Different Start and Stop Codons:
125 </para><para>
126 To specify different sets of start and stop codons, modify the file
127 gene.h . Specifically, the functions:
128 </para><para>
129 Is_Forward_Start Is_Reverse_Start Is_Start
130 Is_Forward_Stop Is_Reverse_Stop Is_Stop
131 </para><para>
132 are used to determine what is used for start and stop codons.
133 </para><para>
134 Is_Start and Is_Stop do simple string comparisons to specify
135 which patterns are used. To add a new pattern, just add the comparison
136 for it. To remove a pattern, comment out or delete the comparison
137 for it.
138 </para><para>
139 The other four functions use a bit comparison to determine start and
140 stop patterns. They represent a codon as a 12-bit pattern, with 4 bits
141 for each base, one bit for each possible value of the bases, T, G, C
142 or A. Thus the bit pattern 0010 0101 1100 represents the base
143 pattern [C] [A or G] [G or T]. By doing bit operations (& | ~) and
144 comparisons, more complicated patterns involving ambiguous reads
145 can be tested efficiently. Simple patterns can be tested as in
146 the current code.
147 </para><para>
148 For example, to insert an additional start codon of CAT requires 3 changes:
149 1. The line
150 || (Codon & 0x218) == Codon
151 should be inserted into Is_Forward_Start , since 0x218 = 0010 0001 1000
152 represents CAT.
153 2. The line
154 || (Codon & 0x184) == Codon
155 should be inserted into Is_Reverse_Start , since 0x184 = 0001 1000 0100
156 represents ATG, which is the reverse-complement of CAT. Alternately,
157 the #define constant ATG_MASK could be used.
158 3. The line
159 || strncmp (S, "cat", 3) == 0
160 should be inserted into Is_Start .
161 </para>
162
163 </refsect1>
164 <refsect1>
165 <title>OPTIONS</title>
166 <variablelist>
167 <varlistentry>
168 <term><option>-g <replaceable>n</replaceable></option></term>
169 <listitem>
170 <para> Set minimum gene length to n. Default is to compute an
171 optimal value automatically. Don't change this unless you
172 know what you're doing.</para>
173 </listitem>
174 </varlistentry>
175 <varlistentry>
176 <term><option>-l</option></term><listitem><para>Regard the genome as linear (not circular), i.e., do not allow
177 genes to "wrap around" the end of the genome.
178 This option works on both glimmer and long-orfs .
179 The default behavior is to regard the genome as circular.</para></listitem>
180 </varlistentry>
181 <varlistentry>
182 <term><option>-o <replaceable>n</replaceable></option></term><listitem><para>Set maximum overlap length to n. Overlaps shorter than this
183 are permitted. (Default is 0 bp.)</para></listitem>
184 </varlistentry>
185 <varlistentry>
186 <term><option>-p <replaceable>n</replaceable></option></term><listitem><para>Set maximum overlap percentage to n%. Overlaps shorter than
187 this percentage of *both* strings are ignored. (Default is 10%.)</para></listitem>
188 </varlistentry>
189 </variablelist>
190 </refsect1>
191 <refsect1>
192 <title>SEE ALSO</title>
193 <para>
194 tigr-glimmer3 (1),
195 tigr-adjust (1),
196 tigr-anomaly (1),
197 tigr-build-icm (1),
198 tigr-check (1),
199 tigr-codon-usage (1),
200 tigr-compare-lists (1),
201 tigr-extract (1),
202 tigr-generate (1),
203 tigr-get-len (1),
204 tigr-get-putative (1),
205 </para>
206 <para>
207 http://www.tigr.org/software/glimmer/
208 </para>
209
210 <para>Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer3.</para>
211 </refsect1>
212 <refsect1>
213 <title>AUTHOR</title>
214
215 <para>This manual page was quickly copied from the glimmer web site by &dhusername; &dhemail; for
216 the &debian; system.
217 </para>
218
219 </refsect1>
220 </refentry>
221
222 <!-- Keep this comment at the end of the file
223 Local variables:
224 mode: sgml
225 sgml-omittag:t
226 sgml-shorttag:t
227 sgml-minimize-attributes:nil
228 sgml-always-quote-attributes:t
229 sgml-indent-step:2
230 sgml-indent-data:t
231 sgml-parent-document:nil
232 sgml-default-dtd-file:nil
233 sgml-exposed-tags:nil
234 sgml-local-catalogs:nil
235 sgml-local-ecat-files:nil
236 End:
237 -->
0 .TH "TIGR-GLIMMER" "1"
1 .SH "NAME"
2 tigr-glimmer \(em Apply the suite of programs within glimmer3 to a a prokaryotic or archean genome.
3 .SH "SYNOPSIS"
4 .PP
5 \fBtigr-run-glimmer3\fR
6 .SH "DESCRIPTION"
7 .PP
8 A shell script that wraps a set of tigr-* utilities of the glimmer package to retrieve coding regions.
9 .SH "SEE ALSO"
10 .PP
11 tigr-glimmer3 (1),
12 tigr-adjust (1),
13 tigr-anomaly (1),
14 tigr-build-icm (1),
15 tigr-check (1),
16 tigr-codon-usage (1),
17 tigr-compare-lists (1),
18 tigr-extract (1),
19 tigr-generate (1),
20 tigr-get-len (1),
21 tigr-get-putative (1),
22 tigr-long-orfs (1),
23 .PP
24 http://www.tigr.org/software/glimmer/
25 .PP
26 Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer3.
27 .SH "AUTHOR"
28 .PP
29 This manual page was quickly copied from the glimmer web site by Steffen Moeller moeller@debian.org for
30 the \fBDebian\fP system.
31
32 .\" created by instant / docbook-to-man
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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@debian.org</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
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 debian/*.1
10 debian/glimmer2_mans/*.1
00 #!/usr/bin/make -f
11
22 export DEB_BUILD_MAINT_OPTIONS = hardening=+all
3
4 MANPAGES=debian/glimmer2_mans/tigr-anomaly.1 \
5 debian/glimmer2_mans/tigr-build-icm.1 \
6 debian/glimmer2_mans/tigr-extract.1 \
7 debian/glimmer2_mans/tigr-glimmer3.1 \
8 debian/glimmer2_mans/tigr-long-orfs.1 \
9 debian/glimmer2_mans/tigr-run-glimmer3.1
10
11 .SUFFIXES: .1 .sgml
12
13 .sgml.1:
14 docbook-to-man $< > $@
153
164 %:
175 dh $@
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0 .TH TIGR-GLIMMER 1 "April 16, 2008"
1 .SH NAME
2 tigr-glimmer \- runs various programs of the TIGR Glimmer suite
3 .SH SYNOPSIS
4 .B tigr-glimmer
5 .B program
6 [arguments]
7 .SH DESCRIPTION
8 This manual page documents briefly the
9 .B tigr-glimmer
10 wrapper to the TIGR Glimmer programs.
11 This manual page was written for the Debian GNU/Linux distribution
12 because upstream does not provide this wrapper and it was invented
13 for Debian to avoid conflicts with other packages that might cause
14 a name space pollution.
15 .PP
16 \fBtigr-glimmer\fP is just a wrapper that invokes the various programs in
17 the TIGR Glimmer software package. You can get more detailed documentation
18 in /usr/share/doc/tigr-glimmer. Please note that the documentation there
19 is a part of the former version Glimmer 2. The version Glimmer 3 has
20 some features that were described in the notes.pdf document inside
21 the documentation directory.
22 .PP
23 The following programs are included: anomaly, build-fixed, build-icm,
24 entropy-profile, entropy-score, extract, glimmer3, long-orfs, multi-extract,
25 score-fixed, start-codon-distrib, test, uncovered and window-acgt.
26 .SH OPTIONS
27 There are no options.
28 .SH EXAMPLES
29 .IP tigr-glimmer\ build-icm
30 .IP tigr-glimmer\ long-orfs
31 .SH SEE ALSO
32 For the pre previously packaged version Glimmer2 some text files from
33 the documentation were turned to man pages for the Debian GNU/Linux
34 distribution by Steffen Moeller <moeller@debian.org>
35 .br
36 .SH AUTHORS
37 This manual page was written by Andreas Tille <tille@debian.org>, for
38 the Debian GNU/Linux system (but may be used by others).