Commit b35cc0190bb0b4791db37e40c4aad6470055005c - tigr-glimmer

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debian/changelog less more

0		tigr-glimmer (3.02b-3) UNRELEASED; urgency=medium
	0	tigr-glimmer (3.02b-3) unstable; urgency=medium
1	1
2	2	[ Steffen Möller ]
3	3	* Updated d/u/metadata

14	14	* Trim trailing whitespace.
15	15	* Wrap long lines in changelog entries: 2.13-1.
16	16	* Refer to specific version of license GPL-2+.
	17	* Do not use docbook-to-man to create manpages
17	18
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
19	20
20	21	tigr-glimmer (3.02b-2) unstable; urgency=medium
21	22

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debian/control less more

3	3	Andreas Tille <tille@debian.org>
4	4	Section: science
5	5	Priority: optional
6		Build-Depends: debhelper-compat (= 12),
7		docbook-to-man
	6	Build-Depends: debhelper-compat (= 12)
8	7	Standards-Version: 4.5.0
9	8	Vcs-Browser: https://salsa.debian.org/med-team/tigr-glimmer
10	9	Vcs-Git: https://salsa.debian.org/med-team/tigr-glimmer.git

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debian/glimmer2_mans/tigr-anomaly.1 less more

	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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~~debian/glimmer2_mans/tigr-anomaly.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@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
113		sgml-minimize-attributes:nil
114		sgml-always-quote-attributes:t
115		sgml-indent-step:2
116		sgml-indent-data:t
117		sgml-parent-document:nil
118		sgml-default-dtd-file:nil
119		sgml-exposed-tags:nil
120		sgml-local-catalogs:nil
121		sgml-local-ecat-files:nil
122		End:
123		-->

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debian/glimmer2_mans/tigr-build-icm.1 less more

	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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~~debian/glimmer2_mans/tigr-build-icm.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>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 >= 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 < 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 <train.seq > 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
149		sgml-minimize-attributes:nil
150		sgml-always-quote-attributes:t
151		sgml-indent-step:2
152		sgml-indent-data:t
153		sgml-parent-document:nil
154		sgml-default-dtd-file:nil
155		sgml-exposed-tags:nil
156		sgml-local-catalogs:nil
157		sgml-local-ecat-files:nil
158		End:
159		-->
160
161

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debian/glimmer2_mans/tigr-extract.1 less more

	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

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~~debian/glimmer2_mans/tigr-extract.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@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> <IDstring>> <start position> <stop position>
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
155		sgml-indent-data:t
156		sgml-parent-document:nil
157		sgml-default-dtd-file:nil
158		sgml-exposed-tags:nil
159		sgml-local-catalogs:nil
160		sgml-local-ecat-files:nil
161		End:
162		-->
163
164

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debian/glimmer2_mans/tigr-glimmer.1 less more

	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).

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debian/glimmer2_mans/tigr-glimmer3.1 less more

	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
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

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	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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~~debian/glimmer2_mans/tigr-long-orfs.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@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		-->

+33

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debian/glimmer2_mans/tigr-run-glimmer3.1 less more

	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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~~debian/glimmer2_mans/tigr-run-glimmer3.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@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		-->

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-1

debian/manpages less more

0		debian/*.1
1	0	debian/glimmer2_mans/*.1

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-12

debian/rules less more

0	0	#!/usr/bin/make -f
1	1
2	2	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 $< > $@
15	3
16	4	%:
17	5	dh $@

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-39

~~debian/tigr-glimmer.1~~ less more

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).