<html><head><title>gp_findorf</title>
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<h1>gp_findorf</h1>
<h2>GP</h2>
<h2>2000</h2>
<h2>NAME</h2>
gp_findorf - print ORFs contained in a sequence
<p><h2>SYNOPSIS</h2>
<strong>gp_findorf</strong> [-m value] [-M value] [-o option] [-c file] [-p type] [-q] [-v] [-d] [-h] [inputfile] [outputfile]
<p><h2>OPTIONS</h2>
<p><dl>
<p><p></p><dt><strong>-m value</strong><dd> set the minimal considered ORF length to <em>value</em> bp.
<p><p></p><dt><strong>-M value</strong><dd> set the maximal considered ORF length to <em>value</em> bp.
<p><p></p><dt><strong>-o</strong><dd> specify output type:
<p><p></p><dt><strong>-o s[equences]</strong><dd> print the protein sequences of the ORFs.
<p><p></p><dt><strong>-o p[ositions]</strong><dd> print the nucleotide positions of the ORFs in the
sequence(s).
<p><p></p><dt><strong>-p</strong><dd> print the codon table and exit
<p><p></p><dt><strong>-c code_file</strong><dd> load codon table modifications from file code_file
<p><p></p><dt><strong>-v</strong><dd> Prints the version information.
<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_findorf</strong> prints out all ORF it is able to retrieve from the
provided sequence(s) in all six reading frames. <strong>gp_findorf</strong> always
prints the longest ORF possible. ORF is defined as a nucleotide
sequence starting with a start codon and ending with a stop codon; the
sequences cannot be degenerated (obviously), but have to be strict DNA
or RNA sequences.
<p>See also <a href="gp_seq2prot.html">gp_seq2prot(1)</a> for additional details.
<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_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_pattern.html">gp_pattern(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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