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"/usr/share/xml/docbook/schema/dtd/4.4/docbookx.dtd" [
<!ENTITY dhfirstname "<firstname>Charles</firstname>">
<!ENTITY dhsurname "<surname>Plessy</surname>">
<!ENTITY dhdate "<date>september 5, 2006</date>">
<!ENTITY dhsection "<manvolnum>1</manvolnum>">
<!ENTITY dhemail "<email>charles-debian-nospam@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> -->
<copyright>
<year>2006</year>
<holder>&dhusername;</holder>
</copyright>
&dhdate;
</refentryinfo>
<refmeta>
&dhucpackage;
&dhsection;
</refmeta>
<refnamediv>
<refname>&dhpackage;</refname>
<refpurpose>Simple greedy multiple alignment of non-coding DNA sequences</refpurpose>
</refnamediv>
<refsynopsisdiv>
<cmdsynopsis>
<command>&dhpackage;</command>
<arg choice="opt">options</arg>
<arg>
<replaceable>inputfile.fasta</replaceable>
</arg>
<arg choice="opt">
<replaceable>inputfile2.fasta ...</replaceable>
</arg>
</cmdsynopsis>
<para>
Each fasta file may contain a single sequence or multiple sequences; all sequences will be aligned together.
</para>
</refsynopsisdiv>
<refsect1>
<title>DESCRIPTION</title>
<para><command>Sigma</command> ("Simple greedy multiple alignment") is an alignment program with a new algorithm and scoring scheme designed specifically for non-coding DNA sequence. It uses a strategy of seeking the best possible gapless local alignments, at each step making the best possible alignment consistent with existing alignments, and scores the significance of the alignment based on the lengths of the aligned fragments and a background model which may be supplied or estimated from an auxiliary file of intergenic DNA. With real data, while "correctness" can't be directly quantified for the alignment, running the PhyloGibbs motif finder on pre-aligned sequence suggests that Sigma's alignments are superior.</para>
</refsect1>
<refsect1>
<title>OPTIONS</title>
<variablelist>
<varlistentry>
<term><option>-A</option>
</term>
<listitem>
<para>Aligned output (compare with <option>-F</option> option) (default: only this).</para>
</listitem>
</varlistentry>
<varlistentry>
<term><option>-b</option>
<parameter>filename</parameter>
</term>
<listitem>
<para>Auxiliary file from which to read background sequences (overridden by <option>-B</option>).</para>
</listitem>
</varlistentry>
<varlistentry>
<term>
<option>-B</option>
<parameter>filename</parameter>
</term>
<listitem>
<para>File containing background probabilities.</para>
</listitem>
</varlistentry>
<varlistentry>
<term><option>-F</option>
</term>
<listitem>
<para>Fasta output (can use both <option>-A</option> and <option>-F</option> in either order).</para>
</listitem>
</varlistentry>
<varlistentry>
<term><option>-n</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>
</listitem>
</varlistentry>
<varlistentry>
<term><option>-x</option>
<parameter>number</parameter>
</term>
<listitem>
<para>Set limit for how probable the match is by chance
(default 0.002, smaller=more stringent).</para>
</listitem>
</varlistentry>
<varlistentry>
<term><option>-help</option>,
<option>--help</option>
</term>
<listitem>
<para>Displays this list of options.</para>
</listitem>
</varlistentry>
</variablelist>
</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@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>
|
