<html><head><title>gp_pattern</title>
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<h1>gp_pattern</h1>
<h2>GP</h2>
<h2>2000</h2>
<h2>NAME</h2>
gp_pattern - computate frequencies of nucleotide patterns
<p><h2>SYNOPSIS</h2>
<strong></strong> [-H] [-q] [-v] [-d] [-h] [inputfile] [outputfile]
<p><h2>OPTIONS</h2>
<p><dl>
<p><p></p><dt><strong>-l value</strong><dd> set pattern length
<p><p></p><dt><strong>-H</strong><dd> Output in HTML mode
<p><p></p><dt><strong>-v</strong><dd> Prints the version information.
<p><p></p><dt><strong>-q</strong><dd> Do not display error messages
<p><p></p><dt><strong>-d</strong><dd> Prints lots of debugging information.
<p><p></p><dt><strong>-h</strong><dd> Shows usage information.
<p><p></p><dt><strong>inputfile</strong><dd> file to proces; if not given, will use standard input
<p><p></p><dt><strong>outputfile</strong><dd> file to write the data to; if not given, will
use standard output
<p></dl>
<p><h2>DESCRIPTION</h2>
<p><strong>gp_dimer</strong> records frequencies of patterns. The pattern length is set with
the <strong>-l</strong> option. Beware: the number of possible patterns grows
exponentially, so setting pattern length greater then 6 can be dangerous. You
must use this program only with DNA/RNA sequences.
<p><h2>SEE ALSO</h2>
<a href="index.html">Genpak(1)</a>
<a href="gp_acc.html">gp_acc(1)</a>
<a href="gp_adjust.html">gp_adjust(1)</a>
<a href="gp_cdndev.html">gp_cdndev(1)</a>
<a href="gp_cusage.html">gp_cusage(1)</a>
<a href="gp_digest.html">gp_digest(1)</a>
<a href="gp_dimer.html">gp_dimer(1)</a>
<a href="gp_findorf.html">gp_findorf(1)</a>
<a href="gp_gc.html">gp_gc(1)</a>
<a href="gp_getseq.html">gp_getseq(1)</a>
<a href="gp_map.html">gp_map(1)</a>
<a href="gp_matrix.html">gp_matrix(1)</a>
<a href="gp_mkmtx.html">gp_mkmtx(1)</a>
<a href="gp_primer.html">gp_primer(1)</a>
<a href="gp_qs.html">gp_qs(1)</a>
<a href="gp_randseq.html">gp_randseq(1)</a>
<a href="gp_seq2prot.html">gp_seq2prot(1)</a>
<a href="gp_slen.html">gp_slen(1)</a>
<a href="gp_tm.html">gp_tm(1)</a>
<a href="gp_trimer.html">gp_trimer(1)</a>
<p><h2>DIAGNOSTICS</h2>
<p>All <strong>Genpak</strong> programs complain in situations you would also complain,
like when they cannot find a sequence you gave them or the sequence is not
valid.
<p>The <strong>Genpak</strong> programs do not write over existing files. I have found this
feature very useful :-)
<p><h2>BUGS</h2>
<p>I'm sure there are plenty left, so please mail me if you find them. I tried
to clean up every bug I could find.
<p><h2>AUTHOR</h2>
<p>January Weiner III
<a href="mailto:january@bioinformatics.org"><january@bioinformatics.org></a>
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