[med-svn] r1199 - trunk/packages/glam2/trunk/debian
charles-guest at alioth.debian.org
charles-guest at alioth.debian.org
Sat Jan 26 13:03:48 UTC 2008
Author: charles-guest
Date: 2008-01-26 13:03:48 +0000 (Sat, 26 Jan 2008)
New Revision: 1199
Added:
trunk/packages/glam2/trunk/debian/glam2-purge.1.xml
Log:
Finished manpages, converted to CDBS.
Added: trunk/packages/glam2/trunk/debian/glam2-purge.1.xml
===================================================================
--- trunk/packages/glam2/trunk/debian/glam2-purge.1.xml (rev 0)
+++ trunk/packages/glam2/trunk/debian/glam2-purge.1.xml 2008-01-26 13:03:48 UTC (rev 1199)
@@ -0,0 +1,168 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<?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"
+ "http://www.oasis-open.org/docbook/xml/4.4/docbookx.dtd" [
+
+<!-- Process this file with an XSLT processor, e.g. xsltproc: -->
+<!-- `xsltproc \
+ -''-nonet \
+ -''-param man.charmap.use.subset "0" \
+ -''-param make.year.ranges "1" \
+ -''-param make.single.year.ranges "1" \
+ manpage.xml' -->
+
+ <!ENTITY dhfirstname "Charles">
+ <!ENTITY dhsurname "Plessy">
+ <!ENTITY dhemail "charles-debian-nospam at plessy.org">
+ <!ENTITY dhusername "&dhfirstname; &dhsurname;">
+ <!ENTITY dhrelease "1056">
+ <!ENTITY dhtitle "glam2 Manual">
+ <!ENTITY dhucpackage "GLAM2-PURGE">
+ <!ENTITY dhpackage "glam2-purge">
+ <!ENTITY dhproduct "GLAM2">
+ <!ENTITY dhsection "1">
+
+]>
+
+<refentry>
+ <refentryinfo>
+ <title>&dhtitle;</title>
+ <!-- Better put a suite name instead of &dhpackage; into productname -->
+ <productname>&dhproduct;</productname>
+ <releaseinfo role="version">&dhrelease;</releaseinfo>
+ <authorgroup>
+ <author>
+ <firstname>Andrew</firstname>
+ <firstname>F</firstname>
+ <surname>Neuwald</surname>
+ <contrib>Author of purge, renamed glam2-purge in Debian.</contrib>
+ </author>
+ </authorgroup>
+ <authorgroup>
+ <author>
+ <firstname>Martin</firstname>
+ <firstname>C</firstname>
+ <surname>Frith</surname>
+ <contrib>Modified purge to be ANSI standard C and improved the user interface.</contrib>
+ </author>
+ <author>
+ <firstname>Timothy</firstname>
+ <firstname>L</firstname>
+ <surname>Bailey</surname>
+ <contrib>Modified purge to be ANSI standard C and improved the user interface.</contrib>
+ </author>
+ </authorgroup>
+ <authorgroup>
+ <author>
+ <firstname>&dhfirstname;</firstname>
+ <surname>&dhsurname;</surname>
+ <contrib>Formatted this manpage in DocBook XML for the Debian distribution.</contrib>
+ <address>
+ <email>&dhemail;</email>
+ </address>
+ </author>
+ </authorgroup>
+ <legalnotice>
+ <para>The source code and the documentation of Purge and GLAM2 are released in the public domain.</para>
+ </legalnotice>
+ </refentryinfo>
+ <refmeta>
+ <refentrytitle>&dhucpackage;</refentrytitle>
+ <manvolnum>&dhsection;</manvolnum>
+ </refmeta>
+ <refnamediv>
+ <refname>&dhpackage;</refname>
+ <refpurpose>Removes redundant sequences from a FASTA file</refpurpose>
+ </refnamediv>
+ <refsynopsisdiv>
+ <cmdsynopsis>
+ <command>&dhpackage;</command>
+ <arg choice="plain"><replaceable>file</replaceable></arg>
+ <arg choice="plain"><option>score</option></arg>
+ <arg choice="opt"><option>options</option></arg>
+ </cmdsynopsis>
+ </refsynopsisdiv>
+
+ <refsect1 id="description">
+ <title>DESCRIPTION</title>
+ <para>
+ <command>glam2-purge</command> is a modified version of Andrew Neuwald's <command>purge</command> program that removes redundant sequences from a FASTA file. This is recommended in order to prevent highly similar sequences distorting the search for motifs. Purge works with either DNA or protein sequences and creates an output file such that no two sequences have a (gapless) local alignment score greater than a threshold specified by the user. The output file is named <file>.<score>. The alignment score is based on the BLOSUM62 matrix for proteins, and on a +5/-1 scoring scheme for DNA. Purge can also be used to mask tandem repeats. It uses the XNU program for this purpose.
+ </para>
+ </refsect1>
+
+ <refsect1 id="options">
+ <title>OPTIONS</title>
+ <variablelist>
+ <!-- Use the variablelist.term.separator and the
+ variablelist.term.break.after parameters to
+ control the term elements. -->
+ <varlistentry>
+ <term><option>-n</option></term>
+ <listitem>
+ <para>Sequences are DNA (default: protein).</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-b</option></term>
+ <listitem>
+ <para>Use blast heuristic method (default for protein).</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-e</option></term>
+ <listitem>
+ <para>Use an exhaustive method (default for DNA).</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-q</option></term>
+ <listitem>
+ <para>Keep first sequence in the set.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-x</option></term>
+ <listitem>
+ <para>Use xnu to mask protein tandem repeats.</para>
+ </listitem>
+ </varlistentry>
+ </variablelist>
+ </refsect1>
+
+ <refsect1 id="see_also">
+ <title>SEE ALSO</title>
+ <!-- In alpabetical order. -->
+ <para><citerefentry>
+ <refentrytitle>glam2</refentrytitle>
+ <manvolnum>1</manvolnum>
+ </citerefentry>, <citerefentry>
+ <refentrytitle>glam2format</refentrytitle>
+ <manvolnum>1</manvolnum>
+ </citerefentry>, <citerefentry>
+ <refentrytitle>glam2mask</refentrytitle>
+ <manvolnum>1</manvolnum>
+ </citerefentry>, <citerefentry>
+ <refentrytitle>glam2scan</refentrytitle>
+ <manvolnum>1</manvolnum>
+ </citerefentry>, <citerefentry>
+ <refentrytitle>xnu</refentrytitle>
+ <manvolnum>1</manvolnum>
+ </citerefentry></para>
+ <para>The full Hypertext documentation of GLAM2 is available online at <ulink url="http://bioinformatics.org.au/glam2/">http://bioinformatics.org.au/glam2/</ulink> or on this computer in <filename class="directory">/usr/share/doc/glam2/</filename>.</para>
+ </refsect1>
+
+ <refsect1 id="ref">
+ <title>REFERENCES</title>
+ <para>
+ Purge was written by Andy Neuwald and is described in more detail in Neuwald et al., "Gibbs motif sampling: detection of bacterial outer membrane protein repeats", Protein Science, 4:1618–1632, 1995. Please cite it if you use Purge.
+ </para>
+ <para>
+ If you use GLAM2, please cite: MC Frith, NFW Saunders, B Kobe, TL Bailey (2008) Discovering sequence motifs with arbitrary insertions and deletions, PLoS Computational Biology (in press).
+ </para>
+ </refsect1>
+</refentry>
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