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

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  <!-- Fill in your name for FIRSTNAME and SURNAME. -->
  <!ENTITY dhfirstname "<firstname>Steffen</firstname>">
  <!ENTITY dhsurname   "<surname>Möller</surname>">
  <!-- Please adjust the date whenever revising the manpage. -->
  <!ENTITY dhdate      "<date>November 10, 2004</date>">
  <!ENTITY dhsection   "<manvolnum>1</manvolnum>">
  <!ENTITY dhemail     "<email>moeller@debian.org</email>">
  <!ENTITY dhusername  "Steffen Moeller">
  <!ENTITY dhucpackage "<refentrytitle>TIGR-GLIMMER</refentrytitle>">
  <!ENTITY dhpackage   "tigr-glimmer">

  <!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>2003</year>
      <holder>&dhusername;</holder>
    </copyright>
    &dhdate;
  </refentryinfo>
  <refmeta>
    &dhucpackage;

    &dhsection;
  </refmeta>
  <refnamediv>
    <refname>&dhpackage;</refname>

    <refpurpose>
Fine start/stop positions of genes in genome sequence
</refpurpose>
  </refnamediv>
  <refsynopsisdiv>
    <cmdsynopsis>
      <command>tigr-extract</command>
	<arg>genome-file <option><replaceable>options</replaceable></option></arg>
    </cmdsynopsis>
  </refsynopsisdiv>
  <refsect1>
    <title>DESCRIPTION</title>
<para>
Program extract takes a FASTA format sequence file and a file
with a list of start/stop positions in that file  (e.g., as produced
by the  long-orfs  program) and extracts and outputs the
specified sequences.
</para><para>
The first command-line argument is the name of the sequence file,
which must be in FASTA format.
</para><para>
The second command-line argument is the name of the coordinate file.
It must contain a list of pairs of positions in the first file, one
per line.  The format of each entry is:
</para><para>  &lt;IDstring>&gt;  &lt;start position>  &lt;stop position&gt;
</para><para>This file should contain no other information, so if you're using
the output of  glimmer  or  long-orfs , you'll have to cut off
header lines.
</para><para>
The output of the program goes to the standard output and has one
line for each line in the coordinate file.  Each line contains
the  IDstring , followed by white space, followed by the substring
of the sequence file specified by the coordinate pair.  Specifically,
the substring starts at the first position of the pair and ends at
the second position (inclusive).  If the first position is bigger
than the second, then the DNA reverse complement of each position
is generated.  Start/stop pairs that "wrap around" the end of the
genome are allowed.
</para>
  </refsect1>
  <refsect1>
    <title>OPTIONS</title>
    <variablelist>
      <varlistentry>
        <term><option>-skip</option></term>
	<listitem>
	<para> makes the output omit the first 3 characters of each sequence, i.e., it skips over the start codon.  This was the behaviour of the previous version of the program.</para>
	</listitem>
      </varlistentry>
      <varlistentry>
       <term><option>-l</option></term><listitem><para>
	   makes the output omit an sequences shorter than  n  characters.
	     n  includes the 3 skipped characters if the  -skip  switch
	      is one.
	   </para></listitem>
      </varlistentry>
    </variablelist>
  </refsect1>
  <refsect1>
    <title>SEE ALSO</title>
    <para>
tigr-glimmer3 (1),
tigr-long-orfs (1),
tigr-adjust (1),
tigr-anomaly	(1),
tigr-build-icm (1),
tigr-check (1),
tigr-codon-usage (1),
tigr-compare-lists (1),
tigr-extract (1),
tigr-generate (1),
tigr-get-len (1),
tigr-get-putative (1),
</para>
<para>
http://www.tigr.org/software/glimmer/
</para>

    <para>Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer3.</para>
  </refsect1>
  <refsect1>
    <title>AUTHOR</title>

    <para>This manual page was quickly copied from the glimmer web site by &dhusername; &dhemail; for
      the &debian; system.
    </para>

  </refsect1>
</refentry>

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