<html><head><title>gp_mkmtx</title>
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<h1>gp_mkmtx</h1>
<h2>GP</h2>
<h2>2000</h2>
<h2>NAME</h2>
gp_mkmtx - calculate frequencies of nucleotides
<p><h2>SYNOPSIS</h2>
<strong>gp_mkmtx</strong> [-a] [-g value] [-l] [-q] [-v] [-d] [-h] [inputfile] [outputfile]
<p><h2>OPTIONS</h2>
<p><dl>
<p><p></p><dt><strong>-a</strong><dd> print only the absolute numbers of occurencies
<p><p></p><dt><strong>-g value</strong><dd> divide each frequency by the expected frequency at GC contents
equal to <strong>value</strong> %.
<p><p></p><dt><strong>-l</strong><dd> do <strong>not</strong> apply logarythmic scaling (as a default, <strong>gp_mkmtx</strong>
calculates the logarythm of the frequencies.
<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_mkmtx</strong> is supposed to be a tool for an easy creation of matrices for the
<a href="gp_matrix.html"><strong>gp_matrix</strong></a> program. It takes a set of sequences,
calculates the frequency of a nucleotide at each position starting from the
first nucleotide and ending with the last nucleotide of the shortest sequence.
For each position, four values are printed in a row, respectively for A, C, G
and T/U. Each value is the logarithm of the calculated frequency
(logarythmisation can be suppresed with the <strong>-l</strong> option). If the <strong>-g</strong>
option is used, prior to the logarithmic scaling the values are diveded by the
expected frequency at the given GC contents (that is, for example, at GC=50%,
0.25 for each nucleotide).
<p><h2>EXAMPLES</h2>
<p>gp_mkmtx -g 50 somesequence.fasta somesequence.mtx
<p>will produce a matrix file somesequence.mtx which, after some editing, will be
directly suitable for the <a href="gp_matrix.html"><strong>gp_matrix</strong></a> program.
<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_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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