Commit 74d639805f19b6b4ea155855cdd938ae0ad35a65 - tigr-glimmer

Fixing version number in manpages Andreas Tille 16 years ago

19 changed file(s) with 532 addition(s) and 544 deletion(s). Raw diff Collapse all Expand all

-1

debian/control less more

4	4	DM-Upload-Allowed: yes
5	5	Uploaders: Steffen Moeller <moeller@debian.org>,
6	6	Andreas Tille <tille@debian.org>
7		Build-Depends: debhelper (>= 5.0), docbook-to-man, gzip, cdbs, quilt
	7	Build-Depends: debhelper (>= 5.0), docbook-to-man, cdbs, quilt
8	8	Standards-Version: 3.7.3
9	9	Homepage: http://www.tigr.org/software/glimmer/
10	10	Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/tigr-glimmer/trunk/?rev=0&sc=0

+139

-139

debian/long-orfs.1 less more

48	48	.ds f2\"
49	49	.ds f3\"
50	50	.ds f4\"
51		'\" t
52		.ta 8n 16n 24n 32n 40n 48n 56n 64n 72n
53		.TH "LONG-ORFS" "1"
54		.SH "NAME"
55		long-orfs \(em Find/Score potential genes in genome-file using
56		the probability model in icm-file
57		.SH "SYNOPSIS"
58		.PP
59		\fBlong-orgs\fR [genome-file \fB\fIoptions\fR\fP]
60		.SH "DESCRIPTION"
61		.PP
62		Program long-orfs takes a sequence file (in FASTA format) and
63		outputs a list of all long "potential genes" in it that do not
64		overlap by too much. By "potential gene" I mean the portion of
65		an orf from the first start codon to the stop codon at the end.
66		.PP
67		The first few lines of output specify the settings of various
68		parameters in the program:
69		.PP
70		Minimum gene length is the length of the smallest fragment
71		considered to be a gene. The length is measured from the first base
72		of the start codon to the last base before the stop codon.
73		This value can be specified when running the program with the -g option.
74		By default, the program now (April 2003) will compute an optimal length
75		for this parameter, where "optimal" is the value that produces the
76		greatest number of long ORFs, thereby increasing the amount of data
77		used for training.
78		.PP
79		Minimum overlap length is a lower bound on the number of bases overlap
80		between 2 genes that is considered a problem. Overlaps shorter than
81		this are ignored.
82		.PP
83		Minimum overlap percent is another lower bound on the number of bases
84		overlap that is considered a problem. Overlaps shorter than this
85		percentage of both genes are ignored.
86		.PP
87		The next portion of the output is a list of potential genes:
88		.PP
89		Column 1 is an ID number for reference purposes. It is assigned
90		sequentially starting with 1 to all long potential genes. If
91		overlapping genes are eliminated, gaps in the numbers will occur.
92		The ID prefix is specified in the constant ID_PREFIX .
93		.PP
94		Column 2 is the position of the first base of the first start codon in
95		the orf. Currently I use atg, and gtg as start codons. This is
96		easily changed in the function Is_Start () .
97		.PP
98		Column 3 is the position of the last base before the stop codon. Stop
99		codons are taa, tag, and tga. Note that for orfs in the reverse
100		reading frames have their start position higher than the end position.
101		The order in which orfs are listed is in increasing order by
102		Max {OrfStart, End}, i.e., the highest numbered position in the orf,
103		except for orfs that "wrap around" the end of the sequence.
104		.PP
105		When two genes with ID numbers overlap by at least a sufficient
106		amount (as determined by Min_Olap and Min_Olap_Percent ), they
107		are eliminated and do not appear in the output.
108		.PP
109		The final output of the program (sent to the standard error file so
110		it does not show up when output is redirected to a file) is the
111		length of the longest orf found.
112		.PP
113
114		Specifying Different Start and Stop Codons:
115		.PP
116		To specify different sets of start and stop codons, modify the file
117		gene.h . Specifically, the functions:
118		.PP
119		Is_Forward_Start Is_Reverse_Start Is_Start
120		Is_Forward_Stop Is_Reverse_Stop Is_Stop
121		.PP
122		are used to determine what is used for start and stop codons.
123		.PP
124		Is_Start and Is_Stop do simple string comparisons to specify
125		which patterns are used. To add a new pattern, just add the comparison
126		for it. To remove a pattern, comment out or delete the comparison
127		for it.
128		.PP
129		The other four functions use a bit comparison to determine start and
130		stop patterns. They represent a codon as a 12-bit pattern, with 4 bits
131		for each base, one bit for each possible value of the bases, T, G, C
132		or A. Thus the bit pattern 0010 0101 1100 represents the base
133		pattern [C] [A or G] [G or T]. By doing bit operations (& \| ~) and
134		comparisons, more complicated patterns involving ambiguous reads
135		can be tested efficiently. Simple patterns can be tested as in
136		the current code.
137		.PP
138		For example, to insert an additional start codon of CAT requires 3 changes:
139		1. The line
140		\|\| (Codon & 0x218) == Codon
141		should be inserted into Is_Forward_Start , since 0x218 = 0010 0001 1000
142		represents CAT.
143		2. The line
144		\|\| (Codon & 0x184) == Codon
145		should be inserted into Is_Reverse_Start , since 0x184 = 0001 1000 0100
146		represents ATG, which is the reverse-complement of CAT. Alternately,
147		the #define constant ATG_MASK could be used.
148		3. The line
149		\|\| strncmp (S, "cat", 3) == 0
150		should be inserted into Is_Start .
151		.SH "OPTIONS"
152		.IP "\fB-g \fIn\fR\fP" 10
153		Set minimum gene length to n. Default is to compute an
154		optimal value automatically. Don't change this unless you
155		know what you're doing.
156		.IP "\fB-l\fP" 10
157		Regard the genome as linear (not circular), i.e., do not allow
158		genes to "wrap around" the end of the genome.
159		This option works on both glimmer and long-orfs .
160		The default behavior is to regard the genome as circular.
161		.IP "\fB-o \fIn\fR\fP" 10
162		Set maximum overlap length to n. Overlaps shorter than this
163		are permitted. (Default is 0 bp.)
164		.IP "\fB-p \fIn\fR\fP" 10
165		Set maximum overlap percentage to n%. Overlaps shorter than
166		this percentage of both strings are ignored. (Default is 10%.)
167		.SH "SEE ALSO"
168		.PP
169		glimmer2 (1),
170		adjust (1),
171		anomaly (1),
172		build-icm (1),
173		check (1),
174		codon-usage (1),
175		compare-lists (1),
176		extract (1),
177		generate (1),
178		get-len (1),
179		get-putative (1),
180		.PP
181		http://www.tigr.org/software/glimmer/
182		.PP
183		Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer2.
184		.SH "AUTHOR"
185		.PP
186		This manual page was quickly copied from the glimmer web site by Steffen Moeller moeller@pzr.uni-rostock.de for
187		the \fBDebian\fP system.
188
189		...\" created by instant / docbook-to-man, Sun 09 Nov 2003, 19:43
	51	'\" t
	52	.ta 8n 16n 24n 32n 40n 48n 56n 64n 72n
	53	.TH "LONG-ORFS" "1"
	54	.SH "NAME"
	55	long-orfs \(em Find/Score potential genes in genome-file using
	56	the probability model in icm-file
	57	.SH "SYNOPSIS"
	58	.PP
	59	\fBlong-orgs\fR [genome-file \fB\fIoptions\fR\fP]
	60	.SH "DESCRIPTION"
	61	.PP
	62	Program long-orfs takes a sequence file (in FASTA format) and
	63	outputs a list of all long "potential genes" in it that do not
	64	overlap by too much. By "potential gene" I mean the portion of
	65	an orf from the first start codon to the stop codon at the end.
	66	.PP
	67	The first few lines of output specify the settings of various
	68	parameters in the program:
	69	.PP
	70	Minimum gene length is the length of the smallest fragment
	71	considered to be a gene. The length is measured from the first base
	72	of the start codon to the last base before the stop codon.
	73	This value can be specified when running the program with the -g option.
	74	By default, the program now (April 2003) will compute an optimal length
	75	for this parameter, where "optimal" is the value that produces the
	76	greatest number of long ORFs, thereby increasing the amount of data
	77	used for training.
	78	.PP
	79	Minimum overlap length is a lower bound on the number of bases overlap
	80	between 2 genes that is considered a problem. Overlaps shorter than
	81	this are ignored.
	82	.PP
	83	Minimum overlap percent is another lower bound on the number of bases
	84	overlap that is considered a problem. Overlaps shorter than this
	85	percentage of both genes are ignored.
	86	.PP
	87	The next portion of the output is a list of potential genes:
	88	.PP
	89	Column 1 is an ID number for reference purposes. It is assigned
	90	sequentially starting with 1 to all long potential genes. If
	91	overlapping genes are eliminated, gaps in the numbers will occur.
	92	The ID prefix is specified in the constant ID_PREFIX .
	93	.PP
	94	Column 2 is the position of the first base of the first start codon in
	95	the orf. Currently I use atg, and gtg as start codons. This is
	96	easily changed in the function Is_Start () .
	97	.PP
	98	Column 3 is the position of the last base before the stop codon. Stop
	99	codons are taa, tag, and tga. Note that for orfs in the reverse
	100	reading frames have their start position higher than the end position.
	101	The order in which orfs are listed is in increasing order by
	102	Max {OrfStart, End}, i.e., the highest numbered position in the orf,
	103	except for orfs that "wrap around" the end of the sequence.
	104	.PP
	105	When two genes with ID numbers overlap by at least a sufficient
	106	amount (as determined by Min_Olap and Min_Olap_Percent ), they
	107	are eliminated and do not appear in the output.
	108	.PP
	109	The final output of the program (sent to the standard error file so
	110	it does not show up when output is redirected to a file) is the
	111	length of the longest orf found.
	112	.PP
	113
	114	Specifying Different Start and Stop Codons:
	115	.PP
	116	To specify different sets of start and stop codons, modify the file
	117	gene.h . Specifically, the functions:
	118	.PP
	119	Is_Forward_Start Is_Reverse_Start Is_Start
	120	Is_Forward_Stop Is_Reverse_Stop Is_Stop
	121	.PP
	122	are used to determine what is used for start and stop codons.
	123	.PP
	124	Is_Start and Is_Stop do simple string comparisons to specify
	125	which patterns are used. To add a new pattern, just add the comparison
	126	for it. To remove a pattern, comment out or delete the comparison
	127	for it.
	128	.PP
	129	The other four functions use a bit comparison to determine start and
	130	stop patterns. They represent a codon as a 12-bit pattern, with 4 bits
	131	for each base, one bit for each possible value of the bases, T, G, C
	132	or A. Thus the bit pattern 0010 0101 1100 represents the base
	133	pattern [C] [A or G] [G or T]. By doing bit operations (& \| ~) and
	134	comparisons, more complicated patterns involving ambiguous reads
	135	can be tested efficiently. Simple patterns can be tested as in
	136	the current code.
	137	.PP
	138	For example, to insert an additional start codon of CAT requires 3 changes:
	139	1. The line
	140	\|\| (Codon & 0x218) == Codon
	141	should be inserted into Is_Forward_Start , since 0x218 = 0010 0001 1000
	142	represents CAT.
	143	2. The line
	144	\|\| (Codon & 0x184) == Codon
	145	should be inserted into Is_Reverse_Start , since 0x184 = 0001 1000 0100
	146	represents ATG, which is the reverse-complement of CAT. Alternately,
	147	the #define constant ATG_MASK could be used.
	148	3. The line
	149	\|\| strncmp (S, "cat", 3) == 0
	150	should be inserted into Is_Start .
	151	.SH "OPTIONS"
	152	.IP "\fB-g \fIn\fR\fP" 10
	153	Set minimum gene length to n. Default is to compute an
	154	optimal value automatically. Don't change this unless you
	155	know what you're doing.
	156	.IP "\fB-l\fP" 10
	157	Regard the genome as linear (not circular), i.e., do not allow
	158	genes to "wrap around" the end of the genome.
	159	This option works on both glimmer and long-orfs .
	160	The default behavior is to regard the genome as circular.
	161	.IP "\fB-o \fIn\fR\fP" 10
	162	Set maximum overlap length to n. Overlaps shorter than this
	163	are permitted. (Default is 0 bp.)
	164	.IP "\fB-p \fIn\fR\fP" 10
	165	Set maximum overlap percentage to n%. Overlaps shorter than
	166	this percentage of both strings are ignored. (Default is 10%.)
	167	.SH "SEE ALSO"
	168	.PP
	169	glimmer3 (1),
	170	adjust (1),
	171	anomaly (1),
	172	build-icm (1),
	173	check (1),
	174	codon-usage (1),
	175	compare-lists (1),
	176	extract (1),
	177	generate (1),
	178	get-len (1),
	179	get-putative (1),
	180	.PP
	181	http://www.tigr.org/software/glimmer/
	182	.PP
	183	Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer3.
	184	.SH "AUTHOR"
	185	.PP
	186	This manual page was quickly copied from the glimmer web site by Steffen Moeller moeller@pzr.uni-rostock.de for
	187	the \fBDebian\fP system.
	188
	189	...\" created by instant / docbook-to-man, Sun 09 Nov 2003, 19:43

-13

debian/manpages less more

0		debian/tigr-adjust.1
1		debian/tigr-anomaly.1
2		debian/tigr-build-icm.1
3		debian/tigr-check.1
4		debian/tigr-codon-usage.1
5		debian/tigr-compare-lists.1
6		debian/tigr-extract.1
7		debian/tigr-generate.1
8		debian/tigr-get-len.1
9		debian/tigr-get-putative.1
10		debian/tigr-glimmer2.1
11		debian/tigr-long-orfs.1
12		debian/tigr-run-glimmer2.1
	0	debian/tigr-*.1

-2

debian/rules less more

5	5	include /usr/share/cdbs/1/rules/debhelper.mk
6	6	include /usr/share/cdbs/1/class/makefile.mk
7	7
8		MANPAGES=debian/tigr-adjust.1 debian/tigr-anomaly.1 debian/tigr-build-icm.1 debian/tigr-check.1 debian/tigr-codon-usage.1 debian/tigr-compare-lists.1 debian/tigr-extract.1 debian/tigr-generate.1 debian/tigr-get-len.1 debian/tigr-get-putative.1 debian/tigr-run-glimmer2.1 debian/tigr-glimmer2.1 debian/tigr-long-orfs.1
	8	MANPAGES=debian/tigr-adjust.1 debian/tigr-anomaly.1 debian/tigr-build-icm.1 debian/tigr-check.1 debian/tigr-codon-usage.1 debian/tigr-compare-lists.1 debian/tigr-extract.1 debian/tigr-generate.1 debian/tigr-get-len.1 debian/tigr-get-putative.1 debian/tigr-run-glimmer3.1 debian/tigr-glimmer3.1 debian/tigr-long-orfs.1
9	9
10	10	.SUFFIXES: .1 .sgml
11	11

13	13	docbook-to-man $< > $@
14	14
15	15	clean::
16		dh_clean $(MANPAGES) tigr-run-glimmer2
	16	dh_clean $(MANPAGES)
17	17	rm -f bin/* lib/* obj/*
18	18
19	19	build/tigr-glimmer:: $(MANPAGES)

-2

debian/tigr-adjust.sgml less more

71	71	<refsect1>
72	72	<title>SEE ALSO</title>
73	73	<para>
74		tigr-glimmer2 (1),
	74	tigr-glimmer3 (1),
75	75	tigr-adjust (1),
76	76	tigr-anomaly (1),
77	77	tigr-build-icm (1),

88	88	http://www.tigr.org/software/glimmer/
89	89	</para>
90	90
91		<para>Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer2.</para>
	91	<para>Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer3.</para>
92	92	</refsect1>
93	93	<refsect1>
94	94	<title>AUTHOR</title>

-2

debian/tigr-anomaly.sgml less more

77	77	<refsect1>
78	78	<title>SEE ALSO</title>
79	79	<para>
80		tigr-glimmer2 (1),
	80	tigr-glimmer3 (1),
81	81	tigr-adjust (1),
82	82	tigr-anomaly (1),
83	83	tigr-build-icm (1),

93	93	http://www.tigr.org/software/glimmer/
94	94	</para>
95	95
96		<para>Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer2.</para>
	96	<para>Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer3.</para>
97	97	</refsect1>
98	98	<refsect1>
99	99	<title>AUTHOR</title>

-3

debian/tigr-build-icm.sgml less more

73	73	</para><para>
74	74	Input comes from the file named on the command-line. Format should be
75	75	one string per line. Each line has an ID string followed by white space
76		followed by the sequence itself. The script run-glimmer2 generates
	76	followed by the sequence itself. The script run-glimmer3 generates
77	77	an input file in the correct format using the 'extract' program.
78	78	</para><para>
79	79	The IMM is constructed as follows: For a given context, say

115	115	<refsect1>
116	116	<title>SEE ALSO</title>
117	117	<para>
118		tigr-glimmer2 (1),
	118	tigr-glimmer3 (1),
119	119	tigr-long-orfs (1),
120	120	tigr-adjust (1),
121	121	tigr-anomaly (1),

129	129	tigr-get-putative (1),
130	130	</para>
131	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 Glimmer2.</para>
	132	<para>Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer3.</para>
133	133	</refsect1>
134	134	<refsect1>
135	135	<title>AUTHOR</title>

-2

debian/tigr-check.sgml less more

71	71	<refsect1>
72	72	<title>SEE ALSO</title>
73	73	<para>
74		tigr-glimmer2 (1),
	74	tigr-glimmer3 (1),
75	75	tigr-adjust (1),
76	76	tigr-anomaly (1),
77	77	tigr-build-icm (1),

87	87	http://www.tigr.org/software/glimmer/
88	88	</para>
89	89
90		<para>Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer2.</para>
	90	<para>Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer3.</para>
91	91	</refsect1>
92	92	<refsect1>
93	93	<title>AUTHOR</title>

-2

debian/tigr-codon-usage.sgml less more

75	75	<refsect1>
76	76	<title>SEE ALSO</title>
77	77	<para>
78		tigr-glimmer2 (1),
	78	tigr-glimmer3 (1),
79	79	tigr-adjust (1),
80	80	tigr-anomaly (1),
81	81	tigr-build-icm (1),

91	91	http://www.tigr.org/software/glimmer/
92	92	</para>
93	93
94		<para>Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer2.</para>
	94	<para>Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer3.</para>
95	95	</refsect1>
96	96	<refsect1>
97	97	<title>AUTHOR</title>

-2

debian/tigr-compare-lists.sgml less more

75	75	<refsect1>
76	76	<title>SEE ALSO</title>
77	77	<para>
78		tigr-glimmer2 (1),
	78	tigr-glimmer3 (1),
79	79	tigr-adjust (1),
80	80	tigr-anomaly (1),
81	81	tigr-build-icm (1),

91	91	http://www.tigr.org/software/glimmer/
92	92	</para>
93	93
94		<para>Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer2.</para>
	94	<para>Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer3.</para>
95	95	</refsect1>
96	96	<refsect1>
97	97	<title>AUTHOR</title>

-2

debian/tigr-extract.sgml less more

115	115	<refsect1>
116	116	<title>SEE ALSO</title>
117	117	<para>
118		tigr-glimmer2 (1),
	118	tigr-glimmer3 (1),
119	119	tigr-long-orfs (1),
120	120	tigr-adjust (1),
121	121	tigr-anomaly (1),

132	132	http://www.tigr.org/software/glimmer/
133	133	</para>
134	134
135		<para>Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer2.</para>
	135	<para>Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer3.</para>
136	136	</refsect1>
137	137	<refsect1>
138	138	<title>AUTHOR</title>

-2

debian/tigr-generate.sgml less more

71	71	<refsect1>
72	72	<title>SEE ALSO</title>
73	73	<para>
74		tigr-glimmer2 (1),
	74	tigr-glimmer3 (1),
75	75	tigr-adjust (1),
76	76	tigr-anomaly (1),
77	77	tigr-build-icm (1),

87	87	http://www.tigr.org/software/glimmer/
88	88	</para>
89	89
90		<para>Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer2.</para>
	90	<para>Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer3.</para>
91	91	</refsect1>
92	92	<refsect1>
93	93	<title>AUTHOR</title>

-2

debian/tigr-get-len.sgml less more

71	71	<refsect1>
72	72	<title>SEE ALSO</title>
73	73	<para>
74		tigr-glimmer2 (1),
	74	tigr-glimmer3 (1),
75	75	tigr-adjust (1),
76	76	tigr-anomaly (1),
77	77	tigr-build-icm (1),

87	87	http://www.tigr.org/software/glimmer/
88	88	</para>
89	89
90		<para>Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer2.</para>
	90	<para>Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer3.</para>
91	91	</refsect1>
92	92	<refsect1>
93	93	<title>AUTHOR</title>

-2

debian/tigr-get-putative.sgml less more

67	67	<refsect1>
68	68	<title>SEE ALSO</title>
69	69	<para>
70		tigr-glimmer2 (1),
	70	tigr-glimmer3 (1),
71	71	tigr-adjust (1),
72	72	tigr-anomaly (1),
73	73	tigr-build-icm (1),

83	83	<para>
84	84	http://www.tigr.org/software/glimmer/
85	85	</para>
86		<para>Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer2.</para>
	86	<para>Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer3.</para>
87	87	</refsect1>
88	88	<refsect1>
89	89	<title>AUTHOR</title>

-246

~~debian/tigr-glimmer2.sgml~~ less more

0		<!doctype refentry PUBLIC "-//OASIS//DTD DocBook V4.1//EN" [
1
2		<!-- Process this file with docbook-to-man to generate an nroff manual
3		page: `docbook-to-man manpage.sgml > manpage.1'. You may view
4		the manual page with: `docbook-to-man manpage.sgml \| nroff -man \|
5		less'. A typical entry in a Makefile or Makefile.am is:
6
7		manpage.1: manpage.sgml
8		docbook-to-man $< > $@
9
10
11		The docbook-to-man binary is found in the docbook-to-man package.
12		Please remember that if you create the nroff version in one of the
13		debian/rules file targets (such as build), you will need to include
14		docbook-to-man in your Build-Depends control field.
15
16		-->
17
18		<!-- Fill in your name for FIRSTNAME and SURNAME. -->
19		<!ENTITY dhfirstname "<firstname>Steffen</firstname>">
20		<!ENTITY dhsurname "<surname>Möller</surname>">
21		<!-- Please adjust the date whenever revising the manpage. -->
22		<!ENTITY dhdate "<date>November 10, 2004</date>">
23		<!ENTITY dhsection "<manvolnum>1</manvolnum>">
24		<!ENTITY dhemail "<email>moeller@pzr.uni-rostock.de</email>">
25		<!ENTITY dhusername "Steffen Moeller">
26		<!ENTITY dhucpackage "<refentrytitle>TIGR-GLIMMER</refentrytitle>">
27		<!ENTITY dhpackage "tigr-glimmer">
28
29		<!ENTITY debian "<productname>Debian</productname>">
30		<!ENTITY gnu "<acronym>GNU</acronym>">
31		<!ENTITY gpl "&gnu; <acronym>GPL</acronym>">
32		]>
33
34		<refentry>
35		<refentryinfo>
36		<address>
37		&dhemail;
38		</address>
39		<author>
40		&dhfirstname;
41		&dhsurname;
42		</author>
43		<copyright>
44		<year>2003</year>
45		<holder>&dhusername;</holder>
46		</copyright>
47		&dhdate;
48		</refentryinfo>
49		<refmeta>
50		&dhucpackage;
51
52		&dhsection;
53		</refmeta>
54		<refnamediv>
55		<refname>&dhpackage;</refname>
56		<refpurpose>
57		Find/Score potential genes in genome-file using the probability model in icm-file
58		</refpurpose>
59		</refnamediv>
60		<refsynopsisdiv>
61		<cmdsynopsis>
62		<command>tigr-glimmer2</command>
63		<arg><option><replaceable>genome-file</replaceable></option></arg>
64		<arg><option><replaceable>icm-file</replaceable></option></arg>
65		<arg><option><replaceable>[options]</replaceable></option></arg>
66		</cmdsynopsis>
67		</refsynopsisdiv>
68		<refsect1>
69		<title>DESCRIPTION</title>
70		<para>
71		<command>&dhpackage;</command> is a system for finding genes in microbial DNA, especially the genomes of bacteria and archaea. <command>&dhpackage;</command> (Gene Locator and Interpolated Markov Modeler) uses interpolated Markov models (IMMs) to identify the coding regions and distinguish them from noncoding DNA. The IMM approach, described in our Nucleic Acids Research paper on <command>&dhpackage;</command> 1.0 and in our subsequent paper on <command>&dhpackage;</command> 2.0, uses a combination of Markov models from 1st through 8th-order, weighting each model according to its predictive power. <command>&dhpackage;</command> 1.0 and 2.0 use 3-periodic nonhomogenous Markov models in their IMMs.
72		</para><para>
73		<command>&dhpackage;</command> is the primary microbial gene finder at TIGR, and has been used to annotate the complete genomes of B. burgdorferi (Fraser et al., Nature, Dec. 1997), T. pallidum (Fraser et al., Science, July 1998), T. maritima, D. radiodurans, M. tuberculosis, and non-TIGR projects including C. trachomatis, C. pneumoniae, and others. Its analyses of some of these genomes and others is available at the TIGR microbial database site.
74		</para><para>
75		A special version of <command>&dhpackage;</command> designed for small eukaryotes, GlimmerM, was used to find the genes in chromosome 2 of the malaria parasite, P. falciparum.. GlimmerM is described in S.L. Salzberg, M. Pertea, A.L. Delcher, M.J. Gardner, and H. Tettelin, "Interpolated Markov models for eukaryotic gene finding," Genomics 59 (1999), 24-31. Click here (http://www.tigr.org/software/glimmerm/) to visit the GlimmerM site, which includes information on how to download the GlimmerM system.
76		</para><para>
77		The <command>&dhpackage;</command> system consists of two main programs. The first of these is the training program, build-imm. This program takes an input set of sequences and builds and outputs the IMM for them. These sequences can be complete genes or just partial orfs. For a new genome, this training data can consist of those genes with strong database hits as well as very long open reading frames that are statistically almost certain to be genes. The second program is glimmer, which uses this IMM to identify putative genes in an entire genome. <command>&dhpackage;</command> automatically resolves conflicts between most overlapping genes by choosing one of them. It also identifies genes that are suspected to truly overlap, and flags these for closer inspection by the user. These ``suspect'' gene candidates have been a very small percentage of the total for all the genomes analyzed thus far.
78		<command>&dhpackage;</command> is a program that...</para>
79		</refsect1>
80		<refsect1>
81		<title>OPTIONS</title>
82		<variablelist>
83		<varlistentry>
84		<term><option>-C <replaceable>n</replaceable></option></term>
85		<listitem>
86		<para>Use n as GC percentage of independent model</para>
87		<para>Note: n should be a percentage, e.g., -C 45.2</para>
88		</listitem>
89		</varlistentry>
90		<varlistentry>
91		<term>-f</term><listitem><para>Use ribosome-binding energy to choose start codon</para></listitem>
92		</varlistentry>
93		<varlistentry>
94		<term><option>+f</option></term><listitem><para>Use first codon in orf as start codon</para></listitem>
95		</varlistentry>
96		<varlistentry>
97		<term><option>-g <replaceable>n</replaceable></option></term><listitem><para>Set minimum gene length to n</para></listitem>
98		</varlistentry>
99		<varlistentry>
100		<term><option>-i <replaceable>filename</replaceable></option></term>
101		<listitem>
102		<para>Use <option><replaceable>filename</replaceable></option>
103		to select regions of bases that are off
104		limits, so that no bases within that area will be examined
105		</para>
106		</listitem>
107		</varlistentry>
108		<varlistentry>
109		<term><option>-l</option></term>
110		<listitem><para>Assume linear rather than circular genome, i.e., no wraparound</para></listitem>
111		</varlistentry>
112		<varlistentry>
113		<term><option>-L <replaceable>filename</replaceable></option></term>
114		<listitem><para>Use filename to specify a list of orfs that should
115		be scored separately, with no overlap rules
116		</para></listitem>
117		</varlistentry>
118		<varlistentry>
119		<term><option>-M</option></term>
120		<listitem><para>Input is a multifasta file of separate genes to be scored
121		separately, with no overlap rules
122		</para>
123		</listitem>
124		</varlistentry>
125		<varlistentry>
126		<term><option>-o <replaceable>n</replaceable></option></term>
127		<listitem>
128		<para>Set minimum overlap length to n. Overlaps shorter than this
129		are ignored.
130		</para></listitem>
131		</varlistentry>
132		<varlistentry>
133		<term><option>-p <replaceable>n</replaceable></option></term>
134		<listitem>
135		<para>
136		Set minimum overlap percentage to n%. Overlaps shorter than this percentage of both strings are ignored.
137		</para>
138		</listitem>
139		</varlistentry>
140		<varlistentry>
141		<term><option>-q <replaceable>n</replaceable></option></term>
142		<listitem>
143		<para>Set the maximum length orf that can be rejected because of
144		the independent probability score column to (n - 1)
145		</para>
146		</listitem>
147		</varlistentry>
148		<varlistentry>
149		<term><option>-r</option></term>
150		<listitem>
151		<para>
152		Don't use independent probability score column
153		</para>
154		</listitem>
155		</varlistentry>
156		<varlistentry>
157		<term><option>+r</option></term>
158		<listitem><para>
159		Use independent probability score column
160		</para>
161		</listitem>
162		</varlistentry>
163		<varlistentry>
164		<term><option>-r</option></term>
165		<listitem>
166		<para>
167		Don't use independent probability score column
168		</para> </listitem> </varlistentry> <varlistentry>
169		<term><option>-s <replaceable>s</replaceable></option></term>
170		<listitem><para> Use string s as the ribosome binding pattern to find start codons.</para>
171		</listitem>
172		</varlistentry>
173		<varlistentry>
174		<term><option>+S</option></term>
175		<listitem>
176		<para>
177		Do use stricter independent intergenic model that doesn't
178		give probabilities to in-frame stop codons. (Option is obsolete
179		since this is now the only behaviour
180		</para> </listitem>
181		</varlistentry>
182		<varlistentry>
183		<term><option>-t <replaceable>n</replaceable></option></term>
184		<listitem><para>
185		Set threshold score for calling as gene to n. If the in-frame
186		score >= n, then the region is given a number and considered
187		a potential gene.
188		</para> </listitem>
189		</varlistentry>
190		<varlistentry>
191		<term><option>-w <replaceable>n</replaceable> </option></term>
192		<listitem><para>
193		Use "weak" scores on tentative genes n or longer. Weak
194		scores ignore the independent probability score.
195		</para></listitem>
196		</varlistentry>
197		</variablelist>
198		</refsect1>
199		<refsect1>
200		<title>SEE ALSO</title>
201		<para>
202		tigr-adjust (1),
203		tigr-anomaly (1),
204		tigr-build-icm (1),
205		tigr-check (1),
206		tigr-codon-usage (1),
207		tigr-compare-lists (1),
208		tigr-extract (1),
209		tigr-generate (1),
210		tigr-get-len (1),
211		tigr-get-putative (1),
212		tigr-glimmer2 (1),
213		tigr-long-orfs (1)
214		</para>
215		<para>
216		http://www.tigr.org/software/glimmer/
217		</para>
218		<para>Please see the readme in /usr/share/doc/glimmer for a description on how to use Glimmer.</para>
219		</refsect1>
220		<refsect1>
221		<title>AUTHOR</title>
222		<para>This manual page was quickly copied from the glimmer web site by &dhusername; &dhemail; for
223		the &debian; system.
224		</para>
225		</refsect1>
226		</refentry>
227
228		<!-- Keep this comment at the end of the file
229		Local variables:
230		mode: sgml
231		sgml-omittag:t
232		sgml-shorttag:t
233		sgml-minimize-attributes:nil
234		sgml-always-quote-attributes:t
235		sgml-indent-step:2
236		sgml-indent-data:t
237		sgml-parent-document:nil
238		sgml-default-dtd-file:nil
239		sgml-exposed-tags:nil
240		sgml-local-catalogs:nil
241		sgml-local-ecat-files:nil
242		End:
243		-->
244
245

+246

-0

debian/tigr-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@pzr.uni-rostock.de</email>">
	25	<!ENTITY dhusername "Steffen Moeller">
	26	<!ENTITY dhucpackage "<refentrytitle>TIGR-GLIMMER</refentrytitle>">
	27	<!ENTITY dhpackage "tigr-glimmer">
	28
	29	<!ENTITY debian "<productname>Debian</productname>">
	30	<!ENTITY gnu "<acronym>GNU</acronym>">
	31	<!ENTITY gpl "&gnu; <acronym>GPL</acronym>">
	32	]>
	33
	34	<refentry>
	35	<refentryinfo>
	36	<address>
	37	&dhemail;
	38	</address>
	39	<author>
	40	&dhfirstname;
	41	&dhsurname;
	42	</author>
	43	<copyright>
	44	<year>2003</year>
	45	<holder>&dhusername;</holder>
	46	</copyright>
	47	&dhdate;
	48	</refentryinfo>
	49	<refmeta>
	50	&dhucpackage;
	51
	52	&dhsection;
	53	</refmeta>
	54	<refnamediv>
	55	<refname>&dhpackage;</refname>
	56	<refpurpose>
	57	Find/Score potential genes in genome-file using the probability model in icm-file
	58	</refpurpose>
	59	</refnamediv>
	60	<refsynopsisdiv>
	61	<cmdsynopsis>
	62	<command>tigr-glimmer3</command>
	63	<arg><option><replaceable>genome-file</replaceable></option></arg>
	64	<arg><option><replaceable>icm-file</replaceable></option></arg>
	65	<arg><option><replaceable>[options]</replaceable></option></arg>
	66	</cmdsynopsis>
	67	</refsynopsisdiv>
	68	<refsect1>
	69	<title>DESCRIPTION</title>
	70	<para>
	71	<command>&dhpackage;</command> is a system for finding genes in microbial DNA, especially the genomes of bacteria and archaea. <command>&dhpackage;</command> (Gene Locator and Interpolated Markov Modeler) uses interpolated Markov models (IMMs) to identify the coding regions and distinguish them from noncoding DNA. The IMM approach, described in our Nucleic Acids Research paper on <command>&dhpackage;</command> 1.0 and in our subsequent paper on <command>&dhpackage;</command> 2.0, uses a combination of Markov models from 1st through 8th-order, weighting each model according to its predictive power. <command>&dhpackage;</command> 1.0 and 2.0 use 3-periodic nonhomogenous Markov models in their IMMs.
	72	</para><para>
	73	<command>&dhpackage;</command> is the primary microbial gene finder at TIGR, and has been used to annotate the complete genomes of B. burgdorferi (Fraser et al., Nature, Dec. 1997), T. pallidum (Fraser et al., Science, July 1998), T. maritima, D. radiodurans, M. tuberculosis, and non-TIGR projects including C. trachomatis, C. pneumoniae, and others. Its analyses of some of these genomes and others is available at the TIGR microbial database site.
	74	</para><para>
	75	A special version of <command>&dhpackage;</command> designed for small eukaryotes, GlimmerM, was used to find the genes in chromosome 2 of the malaria parasite, P. falciparum.. GlimmerM is described in S.L. Salzberg, M. Pertea, A.L. Delcher, M.J. Gardner, and H. Tettelin, "Interpolated Markov models for eukaryotic gene finding," Genomics 59 (1999), 24-31. Click here (http://www.tigr.org/software/glimmerm/) to visit the GlimmerM site, which includes information on how to download the GlimmerM system.
	76	</para><para>
	77	The <command>&dhpackage;</command> system consists of two main programs. The first of these is the training program, build-imm. This program takes an input set of sequences and builds and outputs the IMM for them. These sequences can be complete genes or just partial orfs. For a new genome, this training data can consist of those genes with strong database hits as well as very long open reading frames that are statistically almost certain to be genes. The second program is glimmer, which uses this IMM to identify putative genes in an entire genome. <command>&dhpackage;</command> automatically resolves conflicts between most overlapping genes by choosing one of them. It also identifies genes that are suspected to truly overlap, and flags these for closer inspection by the user. These ``suspect'' gene candidates have been a very small percentage of the total for all the genomes analyzed thus far.
	78	<command>&dhpackage;</command> is a program that...</para>
	79	</refsect1>
	80	<refsect1>
	81	<title>OPTIONS</title>
	82	<variablelist>
	83	<varlistentry>
	84	<term><option>-C <replaceable>n</replaceable></option></term>
	85	<listitem>
	86	<para>Use n as GC percentage of independent model</para>
	87	<para>Note: n should be a percentage, e.g., -C 45.2</para>
	88	</listitem>
	89	</varlistentry>
	90	<varlistentry>
	91	<term>-f</term><listitem><para>Use ribosome-binding energy to choose start codon</para></listitem>
	92	</varlistentry>
	93	<varlistentry>
	94	<term><option>+f</option></term><listitem><para>Use first codon in orf as start codon</para></listitem>
	95	</varlistentry>
	96	<varlistentry>
	97	<term><option>-g <replaceable>n</replaceable></option></term><listitem><para>Set minimum gene length to n</para></listitem>
	98	</varlistentry>
	99	<varlistentry>
	100	<term><option>-i <replaceable>filename</replaceable></option></term>
	101	<listitem>
	102	<para>Use <option><replaceable>filename</replaceable></option>
	103	to select regions of bases that are off
	104	limits, so that no bases within that area will be examined
	105	</para>
	106	</listitem>
	107	</varlistentry>
	108	<varlistentry>
	109	<term><option>-l</option></term>
	110	<listitem><para>Assume linear rather than circular genome, i.e., no wraparound</para></listitem>
	111	</varlistentry>
	112	<varlistentry>
	113	<term><option>-L <replaceable>filename</replaceable></option></term>
	114	<listitem><para>Use filename to specify a list of orfs that should
	115	be scored separately, with no overlap rules
	116	</para></listitem>
	117	</varlistentry>
	118	<varlistentry>
	119	<term><option>-M</option></term>
	120	<listitem><para>Input is a multifasta file of separate genes to be scored
	121	separately, with no overlap rules
	122	</para>
	123	</listitem>
	124	</varlistentry>
	125	<varlistentry>
	126	<term><option>-o <replaceable>n</replaceable></option></term>
	127	<listitem>
	128	<para>Set minimum overlap length to n. Overlaps shorter than this
	129	are ignored.
	130	</para></listitem>
	131	</varlistentry>
	132	<varlistentry>
	133	<term><option>-p <replaceable>n</replaceable></option></term>
	134	<listitem>
	135	<para>
	136	Set minimum overlap percentage to n%. Overlaps shorter than this percentage of both strings are ignored.
	137	</para>
	138	</listitem>
	139	</varlistentry>
	140	<varlistentry>
	141	<term><option>-q <replaceable>n</replaceable></option></term>
	142	<listitem>
	143	<para>Set the maximum length orf that can be rejected because of
	144	the independent probability score column to (n - 1)
	145	</para>
	146	</listitem>
	147	</varlistentry>
	148	<varlistentry>
	149	<term><option>-r</option></term>
	150	<listitem>
	151	<para>
	152	Don't use independent probability score column
	153	</para>
	154	</listitem>
	155	</varlistentry>
	156	<varlistentry>
	157	<term><option>+r</option></term>
	158	<listitem><para>
	159	Use independent probability score column
	160	</para>
	161	</listitem>
	162	</varlistentry>
	163	<varlistentry>
	164	<term><option>-r</option></term>
	165	<listitem>
	166	<para>
	167	Don't use independent probability score column
	168	</para> </listitem> </varlistentry> <varlistentry>
	169	<term><option>-s <replaceable>s</replaceable></option></term>
	170	<listitem><para> Use string s as the ribosome binding pattern to find start codons.</para>
	171	</listitem>
	172	</varlistentry>
	173	<varlistentry>
	174	<term><option>+S</option></term>
	175	<listitem>
	176	<para>
	177	Do use stricter independent intergenic model that doesn't
	178	give probabilities to in-frame stop codons. (Option is obsolete
	179	since this is now the only behaviour
	180	</para> </listitem>
	181	</varlistentry>
	182	<varlistentry>
	183	<term><option>-t <replaceable>n</replaceable></option></term>
	184	<listitem><para>
	185	Set threshold score for calling as gene to n. If the in-frame
	186	score >= n, then the region is given a number and considered
	187	a potential gene.
	188	</para> </listitem>
	189	</varlistentry>
	190	<varlistentry>
	191	<term><option>-w <replaceable>n</replaceable> </option></term>
	192	<listitem><para>
	193	Use "weak" scores on tentative genes n or longer. Weak
	194	scores ignore the independent probability score.
	195	</para></listitem>
	196	</varlistentry>
	197	</variablelist>
	198	</refsect1>
	199	<refsect1>
	200	<title>SEE ALSO</title>
	201	<para>
	202	tigr-adjust (1),
	203	tigr-anomaly (1),
	204	tigr-build-icm (1),
	205	tigr-check (1),
	206	tigr-codon-usage (1),
	207	tigr-compare-lists (1),
	208	tigr-extract (1),
	209	tigr-generate (1),
	210	tigr-get-len (1),
	211	tigr-get-putative (1),
	212	tigr-glimmer3 (1),
	213	tigr-long-orfs (1)
	214	</para>
	215	<para>
	216	http://www.tigr.org/software/glimmer/
	217	</para>
	218	<para>Please see the readme in /usr/share/doc/glimmer for a description on how to use Glimmer.</para>
	219	</refsect1>
	220	<refsect1>
	221	<title>AUTHOR</title>
	222	<para>This manual page was quickly copied from the glimmer web site by &dhusername; &dhemail; for
	223	the &debian; system.
	224	</para>
	225	</refsect1>
	226	</refentry>
	227
	228	<!-- Keep this comment at the end of the file
	229	Local variables:
	230	mode: sgml
	231	sgml-omittag:t
	232	sgml-shorttag:t
	233	sgml-minimize-attributes:nil
	234	sgml-always-quote-attributes:t
	235	sgml-indent-step:2
	236	sgml-indent-data:t
	237	sgml-parent-document:nil
	238	sgml-default-dtd-file:nil
	239	sgml-exposed-tags:nil
	240	sgml-local-catalogs:nil
	241	sgml-local-ecat-files:nil
	242	End:
	243	-->
	244
	245

-2

debian/tigr-long-orfs.sgml less more

191	191	<refsect1>
192	192	<title>SEE ALSO</title>
193	193	<para>
194		tigr-glimmer2 (1),
	194	tigr-glimmer3 (1),
195	195	tigr-adjust (1),
196	196	tigr-anomaly (1),
197	197	tigr-build-icm (1),

207	207	http://www.tigr.org/software/glimmer/
208	208	</para>
209	209
210		<para>Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer2.</para>
	210	<para>Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer3.</para>
211	211	</refsect1>
212	212	<refsect1>
213	213	<title>AUTHOR</title>

-120

~~debian/tigr-run-glimmer2.sgml~~ less more

0		<!doctype refentry PUBLIC "-//OASIS//DTD DocBook V4.1//EN" [
1
2		<!-- Process this file with docbook-to-man to generate an nroff manual
3		page: `docbook-to-man manpage.sgml > manpage.1'. You may view
4		the manual page with: `docbook-to-man manpage.sgml \| nroff -man \|
5		less'. A typical entry in a Makefile or Makefile.am is:
6
7		manpage.1: manpage.sgml
8		docbook-to-man $< > $@
9
10
11		The docbook-to-man binary is found in the docbook-to-man package.
12		Please remember that if you create the nroff version in one of the
13		debian/rules file targets (such as build), you will need to include
14		docbook-to-man in your Build-Depends control field.
15
16		-->
17
18		<!-- Fill in your name for FIRSTNAME and SURNAME. -->
19		<!ENTITY dhfirstname "<firstname>Steffen</firstname>">
20		<!ENTITY dhsurname "<surname>Möller</surname>">
21		<!-- Please adjust the date whenever revising the manpage. -->
22		<!ENTITY dhdate "<date>November 10, 2004</date>">
23		<!ENTITY dhsection "<manvolnum>1</manvolnum>">
24		<!ENTITY dhemail "<email>moeller@pzr.uni-rostock.de</email>">
25		<!ENTITY dhusername "Steffen Moeller">
26		<!ENTITY dhucpackage "<refentrytitle>TIGR-GLIMMER</refentrytitle>">
27		<!ENTITY dhpackage "tigr-glimmer">
28
29		<!ENTITY debian "<productname>Debian</productname>">
30		<!ENTITY gnu "<acronym>GNU</acronym>">
31		<!ENTITY gpl "&gnu; <acronym>GPL</acronym>">
32		]>
33
34		<refentry>
35		<refentryinfo>
36		<address>
37		&dhemail;
38		</address>
39		<author>
40		&dhfirstname;
41		&dhsurname;
42		</author>
43		<copyright>
44		<year>2003</year>
45		<holder>&dhusername;</holder>
46		</copyright>
47		&dhdate;
48		</refentryinfo>
49		<refmeta>
50		&dhucpackage;
51
52		&dhsection;
53		</refmeta>
54		<refnamediv>
55		<refname>&dhpackage;</refname>
56
57		<refpurpose>
58		Apply the suite of programs within glimmer2 to a a prokaryotic or archean genome.
59		</refpurpose>
60		</refnamediv>
61		<refsynopsisdiv>
62		<cmdsynopsis>
63		<command>tigr-run-glimmer2</command>
64		</cmdsynopsis>
65		</refsynopsisdiv>
66		<refsect1>
67		<title>DESCRIPTION</title>
68		<para>
69		A shell script that wraps a set of tigr-* utilities of the glimmer package to retrieve coding regions.
70		</para>
71		</refsect1>
72		<refsect1>
73		<title>SEE ALSO</title>
74		<para>
75		tigr-glimmer2 (1),
76		tigr-adjust (1),
77		tigr-anomaly (1),
78		tigr-build-icm (1),
79		tigr-check (1),
80		tigr-codon-usage (1),
81		tigr-compare-lists (1),
82		tigr-extract (1),
83		tigr-generate (1),
84		tigr-get-len (1),
85		tigr-get-putative (1),
86		tigr-long-orfs (1),
87		</para>
88		<para>
89		http://www.tigr.org/software/glimmer/
90		</para>
91
92		<para>Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer2.</para>
93		</refsect1>
94		<refsect1>
95		<title>AUTHOR</title>
96
97		<para>This manual page was quickly copied from the glimmer web site by &dhusername; &dhemail; for
98		the &debian; system.
99		</para>
100
101		</refsect1>
102		</refentry>
103
104		<!-- Keep this comment at the end of the file
105		Local variables:
106		mode: sgml
107		sgml-omittag:t
108		sgml-shorttag:t
109		sgml-minimize-attributes:nil
110		sgml-always-quote-attributes:t
111		sgml-indent-step:2
112		sgml-indent-data:t
113		sgml-parent-document:nil
114		sgml-default-dtd-file:nil
115		sgml-exposed-tags:nil
116		sgml-local-catalogs:nil
117		sgml-local-ecat-files:nil
118		End:
119		-->

+120

-0

debian/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@pzr.uni-rostock.de</email>">
	25	<!ENTITY dhusername "Steffen Moeller">
	26	<!ENTITY dhucpackage "<refentrytitle>TIGR-GLIMMER</refentrytitle>">
	27	<!ENTITY dhpackage "tigr-glimmer">
	28
	29	<!ENTITY debian "<productname>Debian</productname>">
	30	<!ENTITY gnu "<acronym>GNU</acronym>">
	31	<!ENTITY gpl "&gnu; <acronym>GPL</acronym>">
	32	]>
	33
	34	<refentry>
	35	<refentryinfo>
	36	<address>
	37	&dhemail;
	38	</address>
	39	<author>
	40	&dhfirstname;
	41	&dhsurname;
	42	</author>
	43	<copyright>
	44	<year>2003</year>
	45	<holder>&dhusername;</holder>
	46	</copyright>
	47	&dhdate;
	48	</refentryinfo>
	49	<refmeta>
	50	&dhucpackage;
	51
	52	&dhsection;
	53	</refmeta>
	54	<refnamediv>
	55	<refname>&dhpackage;</refname>
	56
	57	<refpurpose>
	58	Apply the suite of programs within glimmer3 to a a prokaryotic or archean genome.
	59	</refpurpose>
	60	</refnamediv>
	61	<refsynopsisdiv>
	62	<cmdsynopsis>
	63	<command>tigr-run-glimmer3</command>
	64	</cmdsynopsis>
	65	</refsynopsisdiv>
	66	<refsect1>
	67	<title>DESCRIPTION</title>
	68	<para>
	69	A shell script that wraps a set of tigr-* utilities of the glimmer package to retrieve coding regions.
	70	</para>
	71	</refsect1>
	72	<refsect1>
	73	<title>SEE ALSO</title>
	74	<para>
	75	tigr-glimmer3 (1),
	76	tigr-adjust (1),
	77	tigr-anomaly (1),
	78	tigr-build-icm (1),
	79	tigr-check (1),
	80	tigr-codon-usage (1),
	81	tigr-compare-lists (1),
	82	tigr-extract (1),
	83	tigr-generate (1),
	84	tigr-get-len (1),
	85	tigr-get-putative (1),
	86	tigr-long-orfs (1),
	87	</para>
	88	<para>
	89	http://www.tigr.org/software/glimmer/
	90	</para>
	91
	92	<para>Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer3.</para>
	93	</refsect1>
	94	<refsect1>
	95	<title>AUTHOR</title>
	96
	97	<para>This manual page was quickly copied from the glimmer web site by &dhusername; &dhemail; for
	98	the &debian; system.
	99	</para>
	100
	101	</refsect1>
	102	</refentry>
	103
	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	-->