[med-svn] r252 - trunk/packages/sigma-align/trunk/debian
Charles Plessy
charles-guest at alioth.debian.org
Sat Apr 7 08:26:58 UTC 2007
Author: charles-guest
Date: 2007-04-07 08:26:57 +0000 (Sat, 07 Apr 2007)
New Revision: 252
Modified:
trunk/packages/sigma-align/trunk/debian/sigma.1.xml
Log:
updated manpage to match the latest template
Modified: trunk/packages/sigma-align/trunk/debian/sigma.1.xml
===================================================================
--- trunk/packages/sigma-align/trunk/debian/sigma.1.xml 2007-04-07 06:46:41 UTC (rev 251)
+++ trunk/packages/sigma-align/trunk/debian/sigma.1.xml 2007-04-07 08:26:57 UTC (rev 252)
@@ -1,48 +1,96 @@
<?xml version='1.0' encoding='ISO-8859-1'?>
+<?xml-stylesheet type="text/xsl"
+ href="http://docbook.sourceforge.net/release/xsl/current/manpages/docbook.xsl"?>
<!DOCTYPE refentry PUBLIC "-//OASIS//DTD DocBook XML V4.4//EN"
-"/usr/share/xml/docbook/schema/dtd/4.4/docbookx.dtd" [
+ "http://www.oasis-open.org/docbook/xml/4.4/docbookx.dtd" [
+ <!ENTITY dhfirstname "Charles">
+ <!ENTITY dhsurname "Plessy">
+ <!ENTITY dhdate "2007-04-07">
+ <!ENTITY dhsection "1">
+ <!ENTITY dhemail "charles-debian-nospam at plessy.org">
+ <!ENTITY dhusername "&dhfirstname; &dhsurname;">
+ <!ENTITY dhucpackage "SIGMA">
+ <!ENTITY dhpackage "sigma">
+ <!ENTITY dhrelease "1.1">
+ <!ENTITY dhtitle "Manual of Sigma">
- <!ENTITY dhfirstname "<firstname>Charles</firstname>">
- <!ENTITY dhsurname "<surname>Plessy</surname>">
- <!ENTITY dhdate "<date>October 4 , 2006</date>">
- <!ENTITY dhsection "<manvolnum>1</manvolnum>">
- <!ENTITY dhemail "<email>charles-debian-nospam at plessy.org</email>">
- <!ENTITY dhusername "Charles Plessy">
- <!ENTITY dhucpackage "<refentrytitle>SIGMA</refentrytitle>">
- <!ENTITY dhpackage "sigma">
- <!ENTITY debian "<productname>Debian</productname>">
- <!ENTITY gnu "<acronym>GNU</acronym>">
- <!ENTITY gpl "&gnu; <acronym>GPL</acronym>">
]>
-<!-- Copyright 2006 Charles Plessy. You can use, copy, and redistribute this manpage under the GNU GPL. -->
-
<refentry>
<refentryinfo>
- <address>
- &dhemail;
- </address>
-<!-- <author>
- &dhfirstname;
- &dhsurname;
- </author> -->
+ <title>&dhtitle;</title>
+ <productname>&dhpackage;</productname>
+ <releaseinfo role="version">&dhrelease;</releaseinfo>
+ <date>&dhdate;</date>
+ <authorgroup>
+ <author>
+ <firstname>Rahul</firstname>
+ <surname>Siddharthan</surname>
+ <contrib>
+ Wrote sigma. If you're using Sigma for actual research, please let the author know so that he can alert you of bugfixes or new releases.
+ </contrib>
+ <address>
+ <affiliation>
+ <orgname>
+ The Institute of Mathematical Sciences
+ </orgname>
+ <address>
+ <city>Chennai</city>
+ <country>India</country>
+ </address>
+ </affiliation>
+ <email>rsidd at imsc.res.in</email>
+ </address>
+ </author>
+
+ <author>
+ <firstname>&dhfirstname;</firstname>
+ <surname>&dhsurname;</surname>
+ <contrib>
+ Wrote the manpage in DocBook XML for the Debian distribution.
+ </contrib>
+ <address>
+ <email>&dhemail;</email>
+ </address>
+ </author>
+ </authorgroup>
+
<copyright>
<year>2006</year>
+ <year>2007</year>
+ <holder>Rahul Siddharthan</holder>
+ </copyright>
+
+ <copyright>
+ <year>2006</year>
+ <year>2007</year>
<holder>&dhusername;</holder>
</copyright>
- &dhdate;
+
+ <legalnotice>
+ <para>
+ Sigma is free software. You can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation.
+ </para>
+
+ <para>
+ On Debian systems, the complete text of the GNU General Public License can be found in /usr/share/common-licenses/GPL.
+ </para>
+ </legalnotice>
</refentryinfo>
+
<refmeta>
- &dhucpackage;
-
- &dhsection;
+ <refentrytitle>&dhucpackage;</refentrytitle>
+ <manvolnum>&dhsection;</manvolnum>
</refmeta>
+
<refnamediv>
<refname>&dhpackage;</refname>
-
- <refpurpose>Simple greedy multiple alignment of non-coding DNA sequences</refpurpose>
+ <refpurpose>
+ Simple greedy multiple alignment of non-coding DNA sequences
+ </refpurpose>
</refnamediv>
+
<refsynopsisdiv>
<cmdsynopsis>
<command>&dhpackage;</command>
@@ -71,7 +119,9 @@
<variablelist>
<varlistentry>
- <term><option>-A</option>, <option>--aligned_output</option>
+ <term>
+ <option>-A</option>
+ <option>--aligned_output</option>
</term>
<listitem>
<para>Aligned, pretty-printed output (compare
@@ -81,7 +131,9 @@
</varlistentry>
<varlistentry>
- <term><option>-b</option>, <option>--bgprobfile</option>
+ <term>
+ <option>-b</option>
+ <option>--bgprobfile</option>
<parameter>filename</parameter>
</term>
<listitem>
@@ -95,29 +147,31 @@
<varlistentry>
<term>
- <option>-B</option>, <option>--bgseqfile</option>
+ <option>-B</option>
+ <option>--bgseqfile</option>
<parameter>filename</parameter>
</term>
<listitem>
- <para>File containing background probabilities. The format
- is described further below.
+ <para>File containing background probabilities. The format
+ is described further below.</para>
</listitem>
</varlistentry>
<varlistentry>
- <term><option>-C</option></term>, <option>--caps_only</option>
+ <term>
+ <option>-C</option>
+ <option>--caps_only</option>
+ </term>
<listitem>
- <para>Use only upper-case letters in output sequence, for
- compatibility with output of some other programs like
- ClustalW and MLagan. By default, output is mixed-case (as
- in Dialign), and lower-case bases are treated as not
- aligned.
+ <para>Use only upper-case letters in output sequence, for compatibility with output of some other programs like ClustalW and MLagan. By default, output is mixed-case (as in Dialign), and lower-case bases are treated as not aligned.
</para>
</listitem>
</varlistentry>
<varlistentry>
- <term><option>-F</option>, <option>--fasta_output</option>
+ <term>
+ <option>-F</option>
+ <option>--fasta_output</option>
</term>
<listitem>
<para>Multi-fasta output (can use both <option>-A</option>
@@ -126,24 +180,28 @@
</varlistentry>
<varlistentry>
- <term><option>-l</option>, <option>--maxfraglength</option>
- <parameter>number</parameter>
+ <term>
+ <option>-l</option>
+ <option>--maxfraglength</option>
+ <parameter>number</parameter>
</term>
<listitem>
- <para>Pre-fragment very long sequences into pieces of this
- average length, for efficiency. Default = 4000. Smaller =
- faster and more memory-efficient, larger may be better.
+ <para>
+ Pre-fragment very long sequences into pieces of this average length, for efficiency. Default = 4000. Smaller = faster and more memory-efficient, larger may be better.
+ </para>
</listitem>
</varlistentry>
-
<varlistentry>
- <term><option>-n</option>, <option>--ncorrel</option>
- <parameter>number</parameter>
+ <term>
+ <option>-n</option>
+ <option>--ncorrel</option>
+ <parameter>number</parameter>
</term>
<listitem>
- <para>Background correlation (default <parameter>2</parameter>=dinucleotide;
- <parameter>1</parameter>=single-site basecounts, <parameter>0</parameter>=0.25 per base).</para>
+ <para>
+ Background correlation (default <parameter>2</parameter>=dinucleotide; <parameter>1</parameter>=single-site basecounts, <parameter>0</parameter>=0.25 per base).
+ </para>
</listitem>
</varlistentry>
@@ -177,46 +235,13 @@
Using a <quote>background model</quote> appropriate to the sequences being aligned greatly reduces spurious alignments on synthetic data (and, one hopes, on real data too). The simplest way to ensure this is to supply, via the <option>-b</option> parameter, a FASTA-format file containing large quantities of similar sequence data (eg, if one is aligning yeast sequences, supply a file containing all intergenic yeast sequence).
</para>
<para>
- Instead of this, if the single-site and dinucleotide frequencies
- are known already, they may be supplied in a file via the -B
- option. The file format should be: one entry per line, with the
- mononucleotide or dinucleotide (case-insensitive) followed by
- the frequency. (eg, "A 0.3", "AT 0.16", etc on successive
- lines.) A sample file is in the "Background" subdirectory of the
- source distribution. A file like "yeast.nc.3.freq" in the "tests" subdirectory of the MEME source distribution works fine (trinucleotide counts are ignored).
+ Instead of this, if the single-site and dinucleotide frequencies are known already, they may be supplied in a file via the <option>-B</option> option. The file format should be: one entry per line, with the mononucleotide or dinucleotide (case-insensitive) followed by the frequency. (eg, "A 0.3", "AT 0.16", etc on successive lines.) A sample file is in the "Background" subdirectory of the source distribution (on Debian systems, this file can be found in the <filename>/usr/share/doc/sigma-align/Background</filename> directory). A file like "yeast.nc.3.freq" in the "tests" subdirectory of the MEME source distribution works fine (trinucleotide counts are ignored).
</para>
</refsect1>
<refsect1>
- <title>AUTHOR</title>
- <para>
- &dhpackage; was written by Rahul Siddharthan, The Institute of Mathematical Sciences, Chennai, India. If you're using Sigma for actual research, please let the author know so that he can alert you of bugfixes or new releases.
- </para>
- </refsect1>
-
- <refsect1>
<title>REFERENCE</title>
<para>
Please cite Sigma: Rahul Siddharthan (2006) Multiple alignment of weakly-conserved non-coding DNA sequence BMC Bioinformatics 2006, 7:143 doi:10.1186/1471-2105-7-143 Published 16 March 2006, available online at http://www.biomedcentral.com/1471-2105/7/143/</para>
</refsect1>
-
- <refsect1>
- <title>COPYRIGHTS</title>
-
- <para>Copyright (C) 2006 Rahul Siddharthan <email>rsidd at imsc.res.in</email>. Sigma is free software. You can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation.</para>
-
- <para>This manual page was written by &dhusername; &dhemail; for
- the &debian; system (but may be used by others). Permission is
- granted to copy, distribute and/or modify this document under
- the terms of the &gnu; General Public License, Version 2 or any
- later version published by the Free Software Foundation.
- </para>
-
- <para>
- On Debian systems, the complete text of the GNU General Public
- License can be found in /usr/share/common-licenses/GPL.
- </para>
-
- </refsect1>
</refentry>
-
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