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<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
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"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
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<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
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<meta http-equiv="Content-Type" content="text/html; charset=utf-8"/>
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<title>wash/rnacode @ GitHub</title>
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.description { font-size: 1.2em; margin-bottom: 30px; margin-top: 30px; font-style: italic;}
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.download { float: right; }
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pre { background: #000; color: #fff; padding: 15px;}
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</style>
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<a href="http://github.com/wash/rnacode"><img style="position: absolute; top: 0; right: 0; border: 0;" src="http://s3.amazonaws.com/github/ribbons/forkme_right_darkblue_121621.png" alt="Fork me on GitHub" /></a>
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<div id="container">
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<div class="download">
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<a href="http://github.com/wash/rnacode/zipball/master">
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<img border="0" width="90" src="http://github.com/images/modules/download/zip.png"></a>
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<a href="http://github.com/wash/rnacode/tarball/master">
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<img border="0" width="90" src="http://github.com/images/modules/download/tar.png"></a>
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</div>
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<h1><a href="http://github.com/wash/rnacode">rnacode</a>
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<span class="small">by <a href="http://github.com/wash">wash</a></span></h1>
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<div class="description">
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RNAcode - Analyze the protein coding potential in multiple sequence alignments
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</div>
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<p>The purpose of RNA code is to detect protein coding regions in a set of homologous nucleotide sequences. RNAcode relies on evolutionary signatures, mainly synonymous/conservative mutations and conservation of the reading frame. These characteristics indicate negative selection acting on an encoded protein and allow sensitive and specific detection of coding regions.
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RNAcode does not rely on any species specific sequence characteristics whatsoever and does not use any machine learning techniques.
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The only input required for RNAcode is a multiple sequence alignment either in MAF or Clustal W format. RNAcode reports local regions with high coding potential and an associated p-value.
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</p><h2>Install</h2>
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<p>Extract the file and run:
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./configure
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make
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make install (as root)
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See file INSTALL for details</p>
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<h2>License</h2>
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<p>RNAcode is licenced under The GNU General Public License version 3.</p>
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<h2>Authors</h2>
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<p>Stefan Washietl (washietl@ebi.ac.uk)<br/><br/> </p>
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<h2>Contact</h2>
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<p>Stefan Washietl (washietl@ebi.ac.uk)<br/> </p>
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<h2>Download</h2>
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<p>
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You can download this project in either
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<a href="http://github.com/wash/rnacode/zipball/master">zip</a> or
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<a href="http://github.com/wash/rnacode/tarball/master">tar</a> formats.
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</p>
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<p>You can also clone the project with <a href="http://git-scm.com">Git</a>
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by running:
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<pre>$ git clone git://github.com/wash/rnacode</pre>
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</p>
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<div class="footer">
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get the source code on GitHub : <a href="http://github.com/wash/rnacode">wash/rnacode</a>
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</div>
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</div>
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</body>
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</html>

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