[med-svn] r1780 - trunk/packages/tigr-glimmer/trunk/debian
tille at alioth.debian.org
tille at alioth.debian.org
Wed Apr 16 20:50:22 UTC 2008
Author: tille
Date: 2008-04-16 20:50:20 +0000 (Wed, 16 Apr 2008)
New Revision: 1780
Removed:
trunk/packages/tigr-glimmer/trunk/debian/long-orfs.1
trunk/packages/tigr-glimmer/trunk/debian/manpages.links
trunk/packages/tigr-glimmer/trunk/debian/tigr-adjust.sgml
trunk/packages/tigr-glimmer/trunk/debian/tigr-check.sgml
trunk/packages/tigr-glimmer/trunk/debian/tigr-codon-usage.sgml
trunk/packages/tigr-glimmer/trunk/debian/tigr-compare-lists.sgml
trunk/packages/tigr-glimmer/trunk/debian/tigr-generate.sgml
trunk/packages/tigr-glimmer/trunk/debian/tigr-get-len.sgml
trunk/packages/tigr-glimmer/trunk/debian/tigr-get-putative.sgml
Log:
Removed man pages that belong to old executables
Deleted: trunk/packages/tigr-glimmer/trunk/debian/long-orfs.1
===================================================================
--- trunk/packages/tigr-glimmer/trunk/debian/long-orfs.1 2008-04-16 20:48:07 UTC (rev 1779)
+++ trunk/packages/tigr-glimmer/trunk/debian/long-orfs.1 2008-04-16 20:50:20 UTC (rev 1780)
@@ -1,190 +0,0 @@
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-.ta 8n 16n 24n 32n 40n 48n 56n 64n 72n
-.TH "LONG-ORFS" "1"
-.SH "NAME"
-long-orfs \(em Find/Score potential genes in genome-file using
-the probability model in icm-file
-.SH "SYNOPSIS"
-.PP
-\fBlong-orgs\fR [genome-file \fB\fIoptions\fR\fP]
-.SH "DESCRIPTION"
-.PP
-Program long-orfs takes a sequence file (in FASTA format) and
-outputs a list of all long "potential genes" in it that do not
-overlap by too much. By "potential gene" I mean the portion of
-an orf from the first start codon to the stop codon at the end.
-.PP
-The first few lines of output specify the settings of various
-parameters in the program:
-.PP
-Minimum gene length is the length of the smallest fragment
-considered to be a gene. The length is measured from the first base
-of the start codon to the last base *before* the stop codon.
-This value can be specified when running the program with the -g option.
-By default, the program now (April 2003) will compute an optimal length
-for this parameter, where "optimal" is the value that produces the
-greatest number of long ORFs, thereby increasing the amount of data
-used for training.
-.PP
-Minimum overlap length is a lower bound on the number of bases overlap
-between 2 genes that is considered a problem. Overlaps shorter than
-this are ignored.
-.PP
-Minimum overlap percent is another lower bound on the number of bases
-overlap that is considered a problem. Overlaps shorter than this
-percentage of *both* genes are ignored.
-.PP
-The next portion of the output is a list of potential genes:
-.PP
-Column 1 is an ID number for reference purposes. It is assigned
-sequentially starting with 1 to all long potential genes. If
-overlapping genes are eliminated, gaps in the numbers will occur.
-The ID prefix is specified in the constant ID_PREFIX .
-.PP
-Column 2 is the position of the first base of the first start codon in
-the orf. Currently I use atg, and gtg as start codons. This is
-easily changed in the function Is_Start () .
-.PP
-Column 3 is the position of the last base *before* the stop codon. Stop
-codons are taa, tag, and tga. Note that for orfs in the reverse
-reading frames have their start position higher than the end position.
-The order in which orfs are listed is in increasing order by
-Max {OrfStart, End}, i.e., the highest numbered position in the orf,
-except for orfs that "wrap around" the end of the sequence.
-.PP
-When two genes with ID numbers overlap by at least a sufficient
-amount (as determined by Min_Olap and Min_Olap_Percent ), they
-are eliminated and do not appear in the output.
-.PP
-The final output of the program (sent to the standard error file so
-it does not show up when output is redirected to a file) is the
-length of the longest orf found.
-.PP
-
-Specifying Different Start and Stop Codons:
-.PP
-To specify different sets of start and stop codons, modify the file
-gene.h . Specifically, the functions:
-.PP
-Is_Forward_Start Is_Reverse_Start Is_Start
-Is_Forward_Stop Is_Reverse_Stop Is_Stop
-.PP
-are used to determine what is used for start and stop codons.
-.PP
-Is_Start and Is_Stop do simple string comparisons to specify
-which patterns are used. To add a new pattern, just add the comparison
-for it. To remove a pattern, comment out or delete the comparison
-for it.
-.PP
-The other four functions use a bit comparison to determine start and
-stop patterns. They represent a codon as a 12-bit pattern, with 4 bits
-for each base, one bit for each possible value of the bases, T, G, C
-or A. Thus the bit pattern 0010 0101 1100 represents the base
-pattern [C] [A or G] [G or T]. By doing bit operations (& | ~) and
-comparisons, more complicated patterns involving ambiguous reads
-can be tested efficiently. Simple patterns can be tested as in
-the current code.
-.PP
-For example, to insert an additional start codon of CAT requires 3 changes:
-1. The line
-|| (Codon & 0x218) == Codon
-should be inserted into Is_Forward_Start , since 0x218 = 0010 0001 1000
-represents CAT.
-2. The line
-|| (Codon & 0x184) == Codon
-should be inserted into Is_Reverse_Start , since 0x184 = 0001 1000 0100
-represents ATG, which is the reverse-complement of CAT. Alternately,
-the #define constant ATG_MASK could be used.
-3. The line
-|| strncmp (S, "cat", 3) == 0
-should be inserted into Is_Start .
-.SH "OPTIONS"
-.IP "\fB-g \fIn\fR\fP" 10
-Set minimum gene length to n. Default is to compute an
-optimal value automatically. Don't change this unless you
-know what you're doing.
-.IP "\fB-l\fP" 10
-Regard the genome as linear (not circular), i.e., do not allow
-genes to "wrap around" the end of the genome.
-This option works on both glimmer and long-orfs .
-The default behavior is to regard the genome as circular.
-.IP "\fB-o \fIn\fR\fP" 10
-Set maximum overlap length to n. Overlaps shorter than this
-are permitted. (Default is 0 bp.)
-.IP "\fB-p \fIn\fR\fP" 10
-Set maximum overlap percentage to n%. Overlaps shorter than
-this percentage of *both* strings are ignored. (Default is 10%.)
-.SH "SEE ALSO"
-.PP
-glimmer3 (1),
-adjust (1),
-anomaly (1),
-build-icm (1),
-check (1),
-codon-usage (1),
-compare-lists (1),
-extract (1),
-generate (1),
-get-len (1),
-get-putative (1),
-.PP
-http://www.tigr.org/software/glimmer/
-.PP
-Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer3.
-.SH "AUTHOR"
-.PP
-This manual page was quickly copied from the glimmer web site by Steffen Moeller moeller at pzr.uni-rostock.de for
-the \fBDebian\fP system.
-
-...\" created by instant / docbook-to-man, Sun 09 Nov 2003, 19:43
Deleted: trunk/packages/tigr-glimmer/trunk/debian/manpages.links
===================================================================
--- trunk/packages/tigr-glimmer/trunk/debian/manpages.links 2008-04-16 20:48:07 UTC (rev 1779)
+++ trunk/packages/tigr-glimmer/trunk/debian/manpages.links 2008-04-16 20:50:20 UTC (rev 1780)
@@ -1 +0,0 @@
-tigr-glimmer glimmer2
Deleted: trunk/packages/tigr-glimmer/trunk/debian/tigr-adjust.sgml
===================================================================
--- trunk/packages/tigr-glimmer/trunk/debian/tigr-adjust.sgml 2008-04-16 20:48:07 UTC (rev 1779)
+++ trunk/packages/tigr-glimmer/trunk/debian/tigr-adjust.sgml 2008-04-16 20:50:20 UTC (rev 1780)
@@ -1,119 +0,0 @@
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- docbook-to-man $< > $@
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- The docbook-to-man binary is found in the docbook-to-man package.
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- <refsect1>
- <title>DESCRIPTION</title>
-<para>
-</para>
- </refsect1>
- <refsect1>
- <title>SEE ALSO</title>
- <para>
-tigr-glimmer3 (1),
-tigr-adjust (1),
-tigr-anomaly (1),
-tigr-build-icm (1),
-tigr-check (1),
-tigr-codon-usage (1),
-tigr-compare-lists (1),
-tigr-extract (1),
-tigr-generate (1),
-tigr-get-len (1),
-tigr-get-putative (1),
-tigr-long-orfs (1)
-</para>
-<para>
-http://www.tigr.org/software/glimmer/
-</para>
-
- <para>Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer3.</para>
- </refsect1>
- <refsect1>
- <title>AUTHOR</title>
-
- <para>This manual page was quickly copied from the glimmer web site by &dhusername; &dhemail; for
- the &debian; system.
- </para>
-
- </refsect1>
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Deleted: trunk/packages/tigr-glimmer/trunk/debian/tigr-check.sgml
===================================================================
--- trunk/packages/tigr-glimmer/trunk/debian/tigr-check.sgml 2008-04-16 20:48:07 UTC (rev 1779)
+++ trunk/packages/tigr-glimmer/trunk/debian/tigr-check.sgml 2008-04-16 20:50:20 UTC (rev 1780)
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- docbook-to-man $< > $@
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- The docbook-to-man binary is found in the docbook-to-man package.
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- <!-- Fill in your name for FIRSTNAME and SURNAME. -->
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-<para>
-</para>
- </refsect1>
- <refsect1>
- <title>SEE ALSO</title>
- <para>
-tigr-glimmer3 (1),
-tigr-adjust (1),
-tigr-anomaly (1),
-tigr-build-icm (1),
-tigr-check (1),
-tigr-codon-usage (1),
-tigr-compare-lists (1),
-tigr-extract (1),
-tigr-generate (1),
-tigr-get-len (1),
-tigr-get-putative (1),
-</para>
-<para>
-http://www.tigr.org/software/glimmer/
-</para>
-
- <para>Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer3.</para>
- </refsect1>
- <refsect1>
- <title>AUTHOR</title>
-
- <para>This manual page was quickly copied from the glimmer web site by &dhusername; &dhemail; for
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-
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--->
Deleted: trunk/packages/tigr-glimmer/trunk/debian/tigr-codon-usage.sgml
===================================================================
--- trunk/packages/tigr-glimmer/trunk/debian/tigr-codon-usage.sgml 2008-04-16 20:48:07 UTC (rev 1779)
+++ trunk/packages/tigr-glimmer/trunk/debian/tigr-codon-usage.sgml 2008-04-16 20:50:20 UTC (rev 1780)
@@ -1,122 +0,0 @@
-<!doctype refentry PUBLIC "-//OASIS//DTD DocBook V4.1//EN" [
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- page: `docbook-to-man manpage.sgml > manpage.1'. You may view
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-
-manpage.1: manpage.sgml
- docbook-to-man $< > $@
-
-
- The docbook-to-man binary is found in the docbook-to-man package.
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- <!-- Fill in your name for FIRSTNAME and SURNAME. -->
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- </refsynopsisdiv>
- <refsect1>
- <title>DESCRIPTION</title>
-<para>
-</para>
-
- </refsect1>
- <refsect1>
- <title>OPTIONS</title>
- </refsect1>
- <refsect1>
- <title>SEE ALSO</title>
- <para>
-tigr-glimmer3 (1),
-tigr-adjust (1),
-tigr-anomaly (1),
-tigr-build-icm (1),
-tigr-check (1),
-tigr-codon-usage (1),
-tigr-compare-lists (1),
-tigr-extract (1),
-tigr-generate (1),
-tigr-get-len (1),
-tigr-get-putative (1),
-</para>
-<para>
-http://www.tigr.org/software/glimmer/
-</para>
-
- <para>Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer3.</para>
- </refsect1>
- <refsect1>
- <title>AUTHOR</title>
-
- <para>This manual page was quickly copied from the glimmer web site by &dhusername; &dhemail; for
- the &debian; system.
- </para>
-
- </refsect1>
-</refentry>
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-<!-- Keep this comment at the end of the file
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Deleted: trunk/packages/tigr-glimmer/trunk/debian/tigr-compare-lists.sgml
===================================================================
--- trunk/packages/tigr-glimmer/trunk/debian/tigr-compare-lists.sgml 2008-04-16 20:48:07 UTC (rev 1779)
+++ trunk/packages/tigr-glimmer/trunk/debian/tigr-compare-lists.sgml 2008-04-16 20:50:20 UTC (rev 1780)
@@ -1,122 +0,0 @@
-<!doctype refentry PUBLIC "-//OASIS//DTD DocBook V4.1//EN" [
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-<!-- Process this file with docbook-to-man to generate an nroff manual
- page: `docbook-to-man manpage.sgml > manpage.1'. You may view
- the manual page with: `docbook-to-man manpage.sgml | nroff -man |
- less'. A typical entry in a Makefile or Makefile.am is:
-
-manpage.1: manpage.sgml
- docbook-to-man $< > $@
-
-
- The docbook-to-man binary is found in the docbook-to-man package.
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- docbook-to-man in your Build-Depends control field.
-
- -->
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- <!-- Fill in your name for FIRSTNAME and SURNAME. -->
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-<para>
-</para>
-
- </refsect1>
- <refsect1>
- <title>OPTIONS</title>
- </refsect1>
- <refsect1>
- <title>SEE ALSO</title>
- <para>
-tigr-glimmer3 (1),
-tigr-adjust (1),
-tigr-anomaly (1),
-tigr-build-icm (1),
-tigr-check (1),
-tigr-codon-usage (1),
-tigr-compare-lists (1),
-tigr-extract (1),
-tigr-generate (1),
-tigr-get-len (1),
-tigr-get-putative (1),
-</para>
-<para>
-http://www.tigr.org/software/glimmer/
-</para>
-
- <para>Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer3.</para>
- </refsect1>
- <refsect1>
- <title>AUTHOR</title>
-
- <para>This manual page was quickly copied from the glimmer web site by &dhusername; &dhemail; for
- the &debian; system.
- </para>
-
- </refsect1>
-</refentry>
-
-<!-- Keep this comment at the end of the file
-Local variables:
-mode: sgml
-sgml-omittag:t
-sgml-shorttag:t
-sgml-minimize-attributes:nil
-sgml-always-quote-attributes:t
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-sgml-default-dtd-file:nil
-sgml-exposed-tags:nil
-sgml-local-catalogs:nil
-sgml-local-ecat-files:nil
-End:
--->
Deleted: trunk/packages/tigr-glimmer/trunk/debian/tigr-generate.sgml
===================================================================
--- trunk/packages/tigr-glimmer/trunk/debian/tigr-generate.sgml 2008-04-16 20:48:07 UTC (rev 1779)
+++ trunk/packages/tigr-glimmer/trunk/debian/tigr-generate.sgml 2008-04-16 20:50:20 UTC (rev 1780)
@@ -1,118 +0,0 @@
-<!doctype refentry PUBLIC "-//OASIS//DTD DocBook V4.1//EN" [
-
-<!-- Process this file with docbook-to-man to generate an nroff manual
- page: `docbook-to-man manpage.sgml > manpage.1'. You may view
- the manual page with: `docbook-to-man manpage.sgml | nroff -man |
- less'. A typical entry in a Makefile or Makefile.am is:
-
-manpage.1: manpage.sgml
- docbook-to-man $< > $@
-
-
- The docbook-to-man binary is found in the docbook-to-man package.
- Please remember that if you create the nroff version in one of the
- debian/rules file targets (such as build), you will need to include
- docbook-to-man in your Build-Depends control field.
-
- -->
-
- <!-- Fill in your name for FIRSTNAME and SURNAME. -->
- <!ENTITY dhfirstname "<firstname>Steffen</firstname>">
- <!ENTITY dhsurname "<surname>Möller</surname>">
- <!-- Please adjust the date whenever revising the manpage. -->
- <!ENTITY dhdate "<date>November 10, 2004</date>">
- <!ENTITY dhsection "<manvolnum>1</manvolnum>">
- <!ENTITY dhemail "<email>moeller at pzr.uni-rostock.de</email>">
- <!ENTITY dhusername "Steffen Moeller">
- <!ENTITY dhucpackage "<refentrytitle>TIGR-GLIMMER</refentrytitle>">
- <!ENTITY dhpackage "tigr-glimmer">
-
- <!ENTITY debian "<productname>Debian</productname>">
- <!ENTITY gnu "<acronym>GNU</acronym>">
- <!ENTITY gpl "&gnu; <acronym>GPL</acronym>">
-]>
-
-<refentry>
- <refentryinfo>
- <address>
- &dhemail;
- </address>
- <author>
- &dhfirstname;
- &dhsurname;
- </author>
- <copyright>
- <year>2003</year>
- <holder>&dhusername;</holder>
- </copyright>
- &dhdate;
- </refentryinfo>
- <refmeta>
- &dhucpackage;
-
- &dhsection;
- </refmeta>
- <refnamediv>
- <refname>&dhpackage;</refname>
-
- <refpurpose>
-This program lacks a description.
-</refpurpose>
- </refnamediv>
- <refsynopsisdiv>
- <cmdsynopsis>
- <command>tigr-generate</command>
- </cmdsynopsis>
- </refsynopsisdiv>
- <refsect1>
- <title>DESCRIPTION</title>
-<para>
-</para>
- </refsect1>
- <refsect1>
- <title>SEE ALSO</title>
- <para>
-tigr-glimmer3 (1),
-tigr-adjust (1),
-tigr-anomaly (1),
-tigr-build-icm (1),
-tigr-check (1),
-tigr-codon-usage (1),
-tigr-compare-lists (1),
-tigr-extract (1),
-tigr-generate (1),
-tigr-get-len (1),
-tigr-get-putative (1),
-</para>
-<para>
-http://www.tigr.org/software/glimmer/
-</para>
-
- <para>Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer3.</para>
- </refsect1>
- <refsect1>
- <title>AUTHOR</title>
-
- <para>This manual page was quickly copied from the glimmer web site by &dhusername; &dhemail; for
- the &debian; system.
- </para>
-
- </refsect1>
-</refentry>
-
-<!-- Keep this comment at the end of the file
-Local variables:
-mode: sgml
-sgml-omittag:t
-sgml-shorttag:t
-sgml-minimize-attributes:nil
-sgml-always-quote-attributes:t
-sgml-indent-step:2
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-sgml-parent-document:nil
-sgml-default-dtd-file:nil
-sgml-exposed-tags:nil
-sgml-local-catalogs:nil
-sgml-local-ecat-files:nil
-End:
--->
Deleted: trunk/packages/tigr-glimmer/trunk/debian/tigr-get-len.sgml
===================================================================
--- trunk/packages/tigr-glimmer/trunk/debian/tigr-get-len.sgml 2008-04-16 20:48:07 UTC (rev 1779)
+++ trunk/packages/tigr-glimmer/trunk/debian/tigr-get-len.sgml 2008-04-16 20:50:20 UTC (rev 1780)
@@ -1,118 +0,0 @@
-<!doctype refentry PUBLIC "-//OASIS//DTD DocBook V4.1//EN" [
-
-<!-- Process this file with docbook-to-man to generate an nroff manual
- page: `docbook-to-man manpage.sgml > manpage.1'. You may view
- the manual page with: `docbook-to-man manpage.sgml | nroff -man |
- less'. A typical entry in a Makefile or Makefile.am is:
-
-manpage.1: manpage.sgml
- docbook-to-man $< > $@
-
-
- The docbook-to-man binary is found in the docbook-to-man package.
- Please remember that if you create the nroff version in one of the
- debian/rules file targets (such as build), you will need to include
- docbook-to-man in your Build-Depends control field.
-
- -->
-
- <!-- Fill in your name for FIRSTNAME and SURNAME. -->
- <!ENTITY dhfirstname "<firstname>Steffen</firstname>">
- <!ENTITY dhsurname "<surname>Möller</surname>">
- <!-- Please adjust the date whenever revising the manpage. -->
- <!ENTITY dhdate "<date>November 10, 2004</date>">
- <!ENTITY dhsection "<manvolnum>1</manvolnum>">
- <!ENTITY dhemail "<email>moeller at pzr.uni-rostock.de</email>">
- <!ENTITY dhusername "Steffen Moeller">
- <!ENTITY dhucpackage "<refentrytitle>TIGR-GLIMMER</refentrytitle>">
- <!ENTITY dhpackage "tigr-glimmer">
-
- <!ENTITY debian "<productname>Debian</productname>">
- <!ENTITY gnu "<acronym>GNU</acronym>">
- <!ENTITY gpl "&gnu; <acronym>GPL</acronym>">
-]>
-
-<refentry>
- <refentryinfo>
- <address>
- &dhemail;
- </address>
- <author>
- &dhfirstname;
- &dhsurname;
- </author>
- <copyright>
- <year>2003</year>
- <holder>&dhusername;</holder>
- </copyright>
- &dhdate;
- </refentryinfo>
- <refmeta>
- &dhucpackage;
-
- &dhsection;
- </refmeta>
- <refnamediv>
- <refname>&dhpackage;</refname>
-
- <refpurpose>
-This program lacks a description.
-</refpurpose>
- </refnamediv>
- <refsynopsisdiv>
- <cmdsynopsis>
- <command>tigr-get-len</command>
- </cmdsynopsis>
- </refsynopsisdiv>
- <refsect1>
- <title>DESCRIPTION</title>
-<para>
-</para>
- </refsect1>
- <refsect1>
- <title>SEE ALSO</title>
- <para>
-tigr-glimmer3 (1),
-tigr-adjust (1),
-tigr-anomaly (1),
-tigr-build-icm (1),
-tigr-check (1),
-tigr-codon-usage (1),
-tigr-compare-lists (1),
-tigr-extract (1),
-tigr-generate (1),
-tigr-get-len (1),
-tigr-get-putative (1),
-</para>
-<para>
-http://www.tigr.org/software/glimmer/
-</para>
-
- <para>Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer3.</para>
- </refsect1>
- <refsect1>
- <title>AUTHOR</title>
-
- <para>This manual page was quickly copied from the glimmer web site by &dhusername; &dhemail; for
- the &debian; system.
- </para>
-
- </refsect1>
-</refentry>
-
-<!-- Keep this comment at the end of the file
-Local variables:
-mode: sgml
-sgml-omittag:t
-sgml-shorttag:t
-sgml-minimize-attributes:nil
-sgml-always-quote-attributes:t
-sgml-indent-step:2
-sgml-indent-data:t
-sgml-parent-document:nil
-sgml-default-dtd-file:nil
-sgml-exposed-tags:nil
-sgml-local-catalogs:nil
-sgml-local-ecat-files:nil
-End:
--->
Deleted: trunk/packages/tigr-glimmer/trunk/debian/tigr-get-putative.sgml
===================================================================
--- trunk/packages/tigr-glimmer/trunk/debian/tigr-get-putative.sgml 2008-04-16 20:48:07 UTC (rev 1779)
+++ trunk/packages/tigr-glimmer/trunk/debian/tigr-get-putative.sgml 2008-04-16 20:50:20 UTC (rev 1780)
@@ -1,114 +0,0 @@
-<!doctype refentry PUBLIC "-//OASIS//DTD DocBook V4.1//EN" [
-
-<!-- Process this file with docbook-to-man to generate an nroff manual
- page: `docbook-to-man manpage.sgml > manpage.1'. You may view
- the manual page with: `docbook-to-man manpage.sgml | nroff -man |
- less'. A typical entry in a Makefile or Makefile.am is:
-
-manpage.1: manpage.sgml
- docbook-to-man $< > $@
-
-
- The docbook-to-man binary is found in the docbook-to-man package.
- Please remember that if you create the nroff version in one of the
- debian/rules file targets (such as build), you will need to include
- docbook-to-man in your Build-Depends control field.
-
- -->
-
- <!-- Fill in your name for FIRSTNAME and SURNAME. -->
- <!ENTITY dhfirstname "<firstname>Steffen</firstname>">
- <!ENTITY dhsurname "<surname>Möller</surname>">
- <!-- Please adjust the date whenever revising the manpage. -->
- <!ENTITY dhdate "<date>November 10, 2004</date>">
- <!ENTITY dhsection "<manvolnum>1</manvolnum>">
- <!ENTITY dhemail "<email>moeller at pzr.uni-rostock.de</email>">
- <!ENTITY dhusername "Steffen Moeller">
- <!ENTITY dhucpackage "<refentrytitle>TIGR-GLIMMER</refentrytitle>">
- <!ENTITY dhpackage "tigr-glimmer">
-
- <!ENTITY debian "<productname>Debian</productname>">
- <!ENTITY gnu "<acronym>GNU</acronym>">
- <!ENTITY gpl "&gnu; <acronym>GPL</acronym>">
-]>
-
-<refentry>
- <refentryinfo>
- <address>
- &dhemail;
- </address>
- <author>
- &dhfirstname;
- &dhsurname;
- </author>
- <copyright>
- <year>2003</year>
- <holder>&dhusername;</holder>
- </copyright>
- &dhdate;
- </refentryinfo>
- <refmeta>
- &dhucpackage;
-
- &dhsection;
- </refmeta>
- <refnamediv>
- <refname>&dhpackage;</refname>
- <refpurpose>
- </refpurpose>
- </refnamediv>
- <refsynopsisdiv>
- <cmdsynopsis>
- <command>tigr-get-putative</command>
- </cmdsynopsis>
- </refsynopsisdiv>
- <refsect1>
- <title>DESCRIPTION</title>
- </refsect1>
- <refsect1>
- <title>SEE ALSO</title>
- <para>
-tigr-glimmer3 (1),
-tigr-adjust (1),
-tigr-anomaly (1),
-tigr-build-icm (1),
-tigr-check (1),
-tigr-codon-usage (1),
-tigr-compare-lists (1),
-tigr-extract (1),
-tigr-generate (1),
-tigr-get-len (1),
-tigr-get-putative (1),
-tigr-long-orfs (1),
-</para>
-<para>
-http://www.tigr.org/software/glimmer/
-</para>
-<para>Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer3.</para>
- </refsect1>
- <refsect1>
- <title>AUTHOR</title>
-
- <para>This manual page was quickly copied from the glimmer web site by &dhusername; &dhemail; for
- the &debian; system.
- </para>
-
- </refsect1>
-</refentry>
-
-<!-- Keep this comment at the end of the file
-Local variables:
-mode: sgml
-sgml-omittag:t
-sgml-shorttag:t
-sgml-minimize-attributes:nil
-sgml-always-quote-attributes:t
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-sgml-default-dtd-file:nil
-sgml-exposed-tags:nil
-sgml-local-catalogs:nil
-sgml-local-ecat-files:nil
-End:
--->
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