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<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8"/>
<title>wash/rnacode @ GitHub</title>
<style type="text/css">
body {
margin-top: 1.0em;
background-color: #ffffff;
font-family: "helvetica";
color: #000000;
}
#container {
margin: 0 auto;
width: 700px;
}
h1 { font-size: 3.8em; color: #000000; margin-bottom: 3px; }
h1 .small { font-size: 0.4em; }
h1 a { text-decoration: none }
h2 { font-size: 1.5em; color: #000000; }
h3 { text-align: center; color: #000000; }
a { color: #000000; }
.description { font-size: 1.2em; margin-bottom: 30px; margin-top: 30px; font-style: italic;}
.download { float: right; }
pre { background: #000; color: #fff; padding: 15px;}
hr { border: 0; width: 80%; border-bottom: 1px solid #aaa}
.footer { text-align:center; padding-top:30px; font-style: italic; }
</style>
</head>
<body>
<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>
<div id="container">
<div class="download">
<a href="http://github.com/wash/rnacode/zipball/master">
<img border="0" width="90" src="http://github.com/images/modules/download/zip.png"></a>
<a href="http://github.com/wash/rnacode/tarball/master">
<img border="0" width="90" src="http://github.com/images/modules/download/tar.png"></a>
</div>
<h1><a href="http://github.com/wash/rnacode">rnacode</a>
<span class="small">by <a href="http://github.com/wash">wash</a></span></h1>
<div class="description">
RNAcode - Analyze the protein coding potential in multiple sequence alignments
</div>
<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.
RNAcode does not rely on any species specific sequence characteristics whatsoever and does not use any machine learning techniques.
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.
</p><h2>Install</h2>
<p>Extract the file and run:
./configure
make
make install (as root)
See file INSTALL for details</p>
<h2>License</h2>
<p>RNAcode is licenced under The GNU General Public License version 3.</p>
<h2>Authors</h2>
<p>Stefan Washietl ([email protected])<br/><br/> </p>
<h2>Contact</h2>
<p>Stefan Washietl ([email protected])<br/> </p>
<h2>Download</h2>
<p>
You can download this project in either
<a href="http://github.com/wash/rnacode/zipball/master">zip</a> or
<a href="http://github.com/wash/rnacode/tarball/master">tar</a> formats.
</p>
<p>You can also clone the project with <a href="http://git-scm.com">Git</a>
by running:
<pre>$ git clone git://github.com/wash/rnacode</pre>
</p>
<div class="footer">
get the source code on GitHub : <a href="http://github.com/wash/rnacode">wash/rnacode</a>
</div>
</div>
</body>
</html>