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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.AlignAce-module.html">Package AlignAce</a> ::
Module AlignAceStandalone
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<h1 class="epydoc">Module AlignAceStandalone</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.AlignAce.AlignAceStandalone-pysrc.html">source code</a></span></p>
<p>This module provides code to work with the standalone version of
AlignACE, for motif search in DNA sequences.</p>
<p>AlignACE homepage:</p>
<p>http://atlas.med.harvard.edu/</p>
<p>AlignACE Citations:</p>
<p>Computational identification of cis-regulatory elements associated
with groups of functionally related genes in Saccharomyces cerevisiae,
Hughes, JD, Estep, PW, Tavazoie S, & GM Church, Journal of Molecular
Biology 2000 Mar 10;296(5):1205-14.</p>
<p>Finding DNA Regulatory Motifs within Unaligned Non-Coding Sequences
Clustered by Whole-Genome mRNA Quantitation, Roth, FR, Hughes, JD, Estep,
PE & GM Church, Nature Biotechnology 1998 Oct;16(10):939-45.</p>
<p>functions: AlignAce - runs the AlignACE standalone prgram and returns
the ApplicationResult object</p>
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<td><span class="summary-sig"><a href="Bio.AlignAce.AlignAceStandalone-module.html#AlignAce" class="summary-sig-name">AlignAce</a>(<span class="summary-sig-arg">infile</span>,
<span class="summary-sig-arg">cmd</span>=<span class="summary-sig-default"><code class="variable-quote">'</code><code class="variable-string">AlignACE</code><code class="variable-quote">'</code></span>,
<span class="summary-sig-arg">**keywds</span>)</span><br />
Runs AlignACE and returns data.</td>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">AlignAce</span>(<span class="sig-arg">infile</span>,
<span class="sig-arg">cmd</span>=<span class="sig-default"><code class="variable-quote">'</code><code class="variable-string">AlignACE</code><code class="variable-quote">'</code></span>,
<span class="sig-arg">**keywds</span>)</span>
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<p>Runs AlignACE and returns data.</p>
<p>cmd == AlignACE executable infile == sequence file to process</p>
<p>You may pass more parameters to **keywds to change the behavior of the
search. Otherwise, optional values will be chosen by blastall.</p>
<p>numcols number of columns to align (10) expect number of
sites expected in model (10) gcback background fractional GC content
of input sequence (0.38) minpass minimum number of non-improved
passes in phase 1 (200) seed set seed for random number generator
(time) undersample possible sites / (expect * numcols * seedings) (1)
oversample 1/undersample (1)</p>
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