<html><head><title>gp_seq2prot</title>
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<h1>gp_seq2prot</h1>
<h2>GP</h2>
<h2>2000</h2>
<h2>NAME</h2>
gp_seq2prot - translate DNA/RNA to protein sequence
<p><h2>SYNOPSIS</h2>
<strong>gp_seq2prot</strong> [-p] [-c code_file ] [-q] [-v] [-d] [-h] [inputfile] [outputfile]
<p><h2>OPTIONS</h2>
<p><dl>
<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_seq2prot</strong> tries to translate a DNA / RNA sequence into protein
sequence. As a default, it uses the standard translation table
common for most organisms, but you can load your own defaults from
a file using option <strong>-c</strong>. The format of this file is quite
simple: all empty lines or lines starting with a "#" are ignored;
all other lines are supposed to contain a three letter codon,
space, and one letter amino acid code or '0' for a STOP codon. You
can see the full codon table with the option <strong>-p</strong>.
<p>The sequences are supposed to begin with a start codon, but their
ends may vary: if no stop codon is found before the sequence ends,
a warning message is generated, but the output will not be aborted.
<p><h2>EXAMPLES</h2>
<p><dl>
<p><li > Translate sequences from file all.orfs.fasta into protein using the
mycoplasma translation table modification stored in file myco.cdn:
<p><code>gp_seq2prot -c myco.cdn all.orfs.fasta</code>
<p><li > Sample file containing modifications of the translation table:
<p><pre>
# This is the codon table for Mycoplasma pneumoniae
# As you see, you have only to put down the codons which differ from the
# standard code. Blank lines, tabs, and lines starting with a '#' are
# always skipped.
UGA W
</pre>
<p></dl>
<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_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_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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