<html><head><title>gp_qs</title>
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<h1>gp_qs</h1>
<h2>GP</h2>
<h2>2000</h2>
<h2>NAME</h2>
gp_qs - quick DNA / RNA sequence searching
<p><h2>SYNOPSIS</h2>
<strong>gp_qs</strong> [-n [value]] [-m|-p] [-q] [-v] [-d] [-h] sequence [inputfile]
<p><strong>gp_qs</strong> -i [-n [value]] [-m|-p] [-q] [-v] [-d] [-h] inputfile
<p><h2>OPTIONS</h2>
<p><dl>
<p><p></p><dt><strong>-n <value></strong><dd> allow degenerate 5' and 3' ends of the alignment
found. For example, <code>gp_qs -n 2 ATCGATCG</code> will also find <code>CGAT</code>.
The <strong>value</strong> parameter tells how many bases at respective ends can
differ from the sequence string.
<p><p></p><dt><strong>-p, -m</strong><dd> search only plus / only minus strang (this options
cannot be used together).
<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_qs</strong> interface differs from most of the <strong>GP</strong> packages. To
make the every day usage simpler, sequence to be retrieved can be
directly put into the command line, and is only read from standard
input if the option <strong>-i</strong> is used. You cannot directly source the
search sequences from an input file; however this restriction can
be easily circumvented by typing something like <code>cat some_file |
gp_qs -i search_file</code>.
<p>Without the <strong>-i</strong> option, <em>sequence</em> string is mandatory. With
the <strong>-i</strong> option, the <em>inputfile</em> containing the sequence(s) in
which we are looking for our search sequence is mandatory.
<p>Note that the sequences can have wildcards, so you can use, for example,
NNNNNNN as the search string.
<p><h2>EXAMPLES</h2>
<p><dl>
<p><li > Look for the sequence "TAATAT" in file orfs.fasta.
<p><code>gp_qs TAATAT orfs.fasta</code>
<p>or
<p><code>cat orfs.fasta | gp_qs TAATAT</code>
<p><li > search for a sequence from the file promoter.seq, in the file
large_database.fasta:
<p>cat promoter.seq | gp_qs -i large.database.fasta
<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_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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