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<?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 "plessy@debian.org">
<!ENTITY dhusername "&dhfirstname; &dhsurname;">
<!ENTITY dhrelease "1056">
<!ENTITY dhtitle "glam2 Manual">
<!ENTITY dhucpackage "GLAM2SCAN">
<!ENTITY dhpackage "glam2scan">
<!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>Martin</firstname>
<firstname>C</firstname>
<surname>Frith</surname>
<contrib>Author of GLAM2.</contrib>
</author>
<author>
<firstname>Timothy</firstname>
<firstname>L</firstname>
<surname>Bailey</surname>
<contrib>Author of GLAM2.</contrib>
</author>
<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 GLAM2 are released in the public domain.</para>
</legalnotice>
</refentryinfo>
<refmeta>
<refentrytitle>&dhucpackage;</refentrytitle>
<manvolnum>&dhsection;</manvolnum>
</refmeta>
<refnamediv>
<refname>&dhpackage;</refname>
<refpurpose>finds a GLAM2 motif in a database</refpurpose>
</refnamediv>
<refsynopsisdiv>
<cmdsynopsis>
<command>&dhpackage;</command>
<arg choice="opt"><option>options</option></arg>
<arg choice="plain"><option>alphabet</option></arg>
<arg choice="plain"><replaceable>my_motif.glam2</replaceable></arg>
<arg choice="plain"><replaceable>my_seqs.fa</replaceable></arg>
</cmdsynopsis>
<para>An alphabet other than <parameter>p</parameter> or <parameter>n</parameter> is interpreted as the name of an alphabet file.</para>
</refsynopsisdiv>
<refsect1 id="description">
<title>DESCRIPTION</title>
<para>
<command>glam2scan</command> finds matches, in a sequence database, to a motif discovered by <command>glam2</command>. Each match receives a score, indicating how well it fits the motif.
</para>
</refsect1>
<refsect1 id="options">
<title>OPTIONS (default settings)</title>
<variablelist>
<!-- Use the variablelist.term.separator and the
variablelist.term.break.after parameters to
control the term elements. -->
<varlistentry>
<term><option>-h</option></term>
<listitem>
<para>Show all options and their default settings.</para>
</listitem>
</varlistentry>
<varlistentry>
<term><option>-o</option></term>
<listitem>
<para>Output file (<parameter>stdout</parameter>).</para>
</listitem>
</varlistentry>
<varlistentry>
<term><option>-n</option></term>
<listitem>
<para>Number of alignments to report (<parameter>25</parameter>).</para>
</listitem>
</varlistentry>
<varlistentry>
<term><option>-2</option></term>
<listitem>
<para>Examine both strands - forward and reverse complement.</para>
</listitem>
</varlistentry>
<varlistentry>
<term><option>-D</option></term>
<listitem>
<para>Deletion pseudocount (<parameter>0.1</parameter>).</para>
</listitem>
</varlistentry>
<varlistentry>
<term><option>-E</option></term>
<listitem>
<para>No-deletion pseudocount (<parameter>2.0</parameter>).</para>
</listitem>
</varlistentry>
<varlistentry>
<term><option>-I</option></term>
<listitem>
<para>Insertion pseudocount (<parameter>0.02</parameter>).</para>
</listitem>
</varlistentry>
<varlistentry>
<term><option>-J</option></term>
<listitem>
<para>No-insertion pseudocount (<parameter>1.0</parameter>).</para>
</listitem>
</varlistentry>
<varlistentry>
<term><option>-d</option></term>
<listitem>
<para>Dirichlet mixture file.</para>
</listitem>
</varlistentry>
</variablelist>
</refsect1>
<refsect1 id="see_also">
<title>SEE ALSO</title>
<!-- In alpabetical order. -->
<para><citerefentry>
<refentrytitle>glam2format</refentrytitle>
<manvolnum>1</manvolnum>
</citerefentry>, <citerefentry>
<refentrytitle>glam2mask</refentrytitle>
<manvolnum>1</manvolnum>
</citerefentry>, <citerefentry>
<refentrytitle>glam2-purge</refentrytitle>
<manvolnum>1</manvolnum>
</citerefentry>, <citerefentry>
<refentrytitle>glam2</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>REFERENCE</title>
<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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