<!doctype refentry PUBLIC "-//OASIS//DTD DocBook V4.1//EN" [

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  <!-- Fill in your name for FIRSTNAME and SURNAME. -->
  <!ENTITY dhfirstname "<firstname>Philipp</firstname>">
  <!ENTITY dhsurname   "<surname>Benner</surname>">
  <!-- Please adjust the date whenever revising the manpage. -->
  <!ENTITY dhdate      "<date>July 2006</date>">
  <!-- SECTION should be 1-8, maybe w/ subsection other parameters are
       allowed: see man(7), man(1). -->
  <!ENTITY dhsection   "<manvolnum>1</manvolnum>">
  <!ENTITY dhemail     "<email>mail@philipp-benner.de</email>">
  <!ENTITY dhusername  "Philipp Benner">
  <!ENTITY dhucpackage "<refentrytitle>DBA</refentrytitle>">
  <!ENTITY dhpackage   "dba">

  <!ENTITY debian      "<productname>Debian</productname>">
  <!ENTITY gnu         "<acronym>GNU</acronym>">
  <!ENTITY gpl         "&gnu; <acronym>GPL</acronym>">
]>

<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>characterising shared regulatory regions of genomic DNA</refpurpose>
  </refnamediv>
  <refsynopsisdiv>
    <cmdsynopsis>
      <command>&dhpackage;</command>

      <group choice=opt>
        <arg rep=repeat><replaceable>options</replaceable></arg>
      </group>

      <group choice=req>
<!-- 	<arg rep=repeat><replaceable>seq1</replaceable></arg> -->
<!-- 	<arg rep=repeat><replaceable>seq2</replaceable></arg> -->
	<arg><replaceable> seq1 seq2</replaceable></arg>
      </group>

    </cmdsynopsis>
  </refsynopsisdiv>
  <refsect1>
    <title>DESCRIPTION</title>

    <para>dba - standing for Dna Block Aligner, was developed by Niclas Jareborg,
    Richard Durbin and Ewan Birney for characterising shared regulatory regions
    of genomic DNA, either in upstream regions or introns of genes</para>

    <para>The idea was that in these regions there would a series of shared motifs,
    perhaps with one or two insertions or deletions but between motifs there
    would be any length of sequence.</para>
    
    <para>The subsquent model was a 3 state model which was log-odd'd ratio to a null
    model of their being no examples of a motif in the two sequences.</para>

  </refsect1>
  <refsect1>
    <title>OPTIONS</title>

    <variablelist>
      <varlistentry>
        <term><option>-h</option>
          <option>-help</option>
        </term>
        <listitem>
          <para>Show summary of options.</para>
        </listitem>
      </varlistentry>
      <varlistentry>
        <term><option>-v</option>
          <option>-version</option>
        </term>
        <listitem>
          <para>Show version of program.</para>
        </listitem>
      </varlistentry>
    </variablelist>
  </refsect1>
  <refsect1>
    <title>SEE ALSO</title>

    <para>dnal (1), estwise (1), estwisedb (1), genewise (1), genewisedb (1), genomewise (1), promoterwise (1), psw (1), pswdb (1), scanwise (1), scanwise_server (1).</para>
  </refsect1>
  <refsect1>
    <title>AUTHOR</title>

    <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 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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