File: glam2.1.xml

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glam2 1064-9
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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 "GLAM2">
  <!ENTITY dhpackage   "glam2">
  <!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>Gapped Local Alignment of Motifs</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_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>
      GLAM2 is a software package for finding motifs in sequences, typically amino-acid or nucleotide sequences. A motif is a re-occurring sequence pattern: typical examples are the TATA box and the CAAX prenylation motif. The main innovation of GLAM2 is that it allows insertions and deletions in motifs.
    </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>-r</option></term>
				<listitem>
					<para>Number of alignment runs (<parameter>10</parameter>).</para>
				</listitem>
			</varlistentry>

			<varlistentry>
				<term><option>-n</option></term>
				<listitem>
					<para>End each run after this many iterations without improvement (<parameter>10000</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>-z</option></term>
				<listitem>
					<para>Minimum number of sequences in the alignment (<parameter>2</parameter>).</para>
				</listitem>
			</varlistentry>

			<varlistentry>
				<term><option>-a</option></term>
				<listitem>
					<para>Minimum number of aligned columns (<parameter>2</parameter>).</para>
				</listitem>
			</varlistentry>

			<varlistentry>
				<term><option>-b</option></term>
				<listitem>
					<para>Maximum number of aligned columns (<parameter>50</parameter>).</para>
				</listitem>
			</varlistentry>

			<varlistentry>
				<term><option>-w</option></term>
				<listitem>
					<para>Initial number of aligned columns (<parameter>20</parameter>).</para>
				</listitem>
			</varlistentry>

			<varlistentry>
				<term><option>-d</option></term>
				<listitem>
					<para>Dirichlet mixture file.</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>-q</option></term>
				<listitem>
					<para>Weight for generic versus sequence-set-specific residue abundances (<parameter>1e+99</parameter>).</para>
				</listitem>
			</varlistentry>

			<varlistentry>
				<term><option>-t</option></term>
				<listitem>
					<para>Initial temperature (<parameter>1.2</parameter>).</para>
				</listitem>
			</varlistentry>
      
			<varlistentry>
				<term><option>-c</option></term>
				<listitem>
					<para>Cooling factor per n iterations (<parameter>1.44</parameter>).</para>
				</listitem>
			</varlistentry>
      
			<varlistentry>
				<term><option>-u</option></term>
				<listitem>
					<para>Temperature lower bound (<parameter>0.1</parameter>).</para>
				</listitem>
			</varlistentry>
      
			<varlistentry>
				<term><option>-p</option></term>
				<listitem>
					<para>Print progress information at each iteration.</para>
				</listitem>
			</varlistentry>
      
			<varlistentry>
				<term><option>-m</option></term>
				<listitem>
					<para>Column-sampling moves per site-sampling move (<parameter>1.0</parameter>).</para>
				</listitem>
			</varlistentry>
      
			<varlistentry>
				<term><option>-x</option></term>
				<listitem>
					<para>Site sampling algorithm: <parameter>0</parameter>=FAST <parameter>1</parameter>=SLOW <parameter>2</parameter>=FFT (<parameter>0</parameter>).</para>
				</listitem>
			</varlistentry>
      
			<varlistentry>
				<term><option>-s</option></term>
				<listitem>
					<para>Seed for pseudo-random numbers (<parameter>1</parameter>).</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>glam2scan</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>