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author davidmurphy
date Thu, 27 Oct 2011 12:09:09 -0400
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+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN"
+    "http://www.w3.org/TR/html4/transitional.dtd">
+<html>
+<head>
+<link rel="stylesheet" type="text/css" href="logo.css" >
+<title>CodonLogo - About</title>
+<meta name="author" content="Gavin E. Crooks" >
+</head>
+
+<body style="align: center">
+
+
+
+
+<table width="80%" border = '0' cellspacing='0' cellpadding='1' align="center">
+<tr><td >
+<h1>CodonLogo 1.0</h1>
+
+</td><td align = "right"> 
+    &middot; 
+  <a class="selected" href="./">about</a>&nbsp;&middot;
+  <a href="create.cgi">create</a>&nbsp;&middot; 
+  <a href="examples.html">examples</a>&nbsp;&middot; 
+  <a href="manual.html">manual</a>&nbsp;&middot; 
+<br>
+<span style="font-size:small">&nbsp;</span>&nbsp;&nbsp;
+
+</td></tr>
+
+
+
+<tr><td colspan="2" style="font-size:small">
+	  <a href="examples.html"><img
+	  alt="CodonLogo" width="284" height="359"
+	  src="img/Replacethis1.png" align="right" vspace="40" hspace="10"></a>
+
+
+<h3>Introduction</h3>
+<p>
+Codonlogo is based on <a href="http://weblogo.berkeley.edu/">WebLogo</a>,a web based application designed to make the 
+generation of sequence logos easy and painless.CodonLogo Extends Weblogo to allow generation of sequence logos with codons rather than amino acids or nucleotides.
+ </p>
+
+<p>
+<a href="http://www.lecb.ncifcrf.gov/~toms/sequencelogo.html">Sequence&nbsp;logos</a> are a graphical representation of an amino acid
+or nucleic acid multiple sequence alignment developed by 
+<a href="http://www.lecb.ncifcrf.gov/~toms/schneider.html">Tom Schneider</a>
+ and <a href="http://www.lecb.ncifcrf.gov/~toms/sipinfo.html">Mike
+ Stephens</a>.
+Each logo consists of stacks of symbols, one stack for each position in the
+sequence. The overall height of the stack indicates the sequence conservation
+at that position, while the height of symbols within the stack indicates the
+relative frequency of each codon at that position. In general,
+a sequence logo provides a richer and more precise description of, for example,
+a binding site, than would a consensus sequence. 
+</p>
+
+<ul> 
+<li><a href="create.cgi">Create your own logos </a>
+</li><li><a href="examples.html">View example sequence logos and input data.</a>
+</li><li><a href="manual.html">Read the User's Manual</a>
+</li><li> <a href="http://code.google.com/p/weblogo/"> Download WebLogo source code</a> 
+</li><li>  <a href="http://groups.google.com/group/WebLogo">WebLogo discussion group</a> 
+</li>
+</ul>
+ 
+
+<h3>References</h3>
+
+
+<p>
+<small>
+<a href="http://bespoke.lbl.gov/">Crooks GE</a>, 
+<a href="http://compbio.berkeley.edu/">Hon G</a>, 
+<a href="http://compbio.berkeley.edu/">Chandonia JM</a>,
+<a href="http://compbio.berkeley.edu/people/brenner/">Brenner SE</a> 
+CodonLogo: A sequence logo 
+generator, <br >
+<em>Genome Research</em>, 14:1188-1190, (2004) 
+[<a href="http://bespoke.lbl.gov/pubs/fulltext/Crooks2004a-GR-WebLogo.pdf">Full Text</a> ]
+</small>
+</p>
+
+<p>
+<small>
+Schneider TD, Stephens RM. 1990.
+<a class="out" href="http://www.lecb.ncifcrf.gov/~toms/paper/logopaper/">Sequence Logos: A New Way to Display Consensus Sequences.</a>
+<em>Nucleic Acids Res.</em> <em>18</em>:6097-6100
+</small>
+</p>
+
+
+
+
+
+<h3>Disclaimer</h3>
+
+<p>
+While no permanent records are kept of submitted sequences, we cannot 
+undertake to guarantee that data sent to CodonLogo remains secure. Moreover,
+no guarantees whatsoever are provided about data generated by CodonLogo. 
+</p>
+
+
+
+<h3>Feedback</h3>
+<p>
+Suggestions on how to improve CodonLogo are heartily welcomed! 
+Please direct questions to murphy.david@gmail.com 
+</p>
+
+</td></tr>
+
+
+
+</table>
+<script type="text/javascript">
+var gaJsHost = (("https:" == document.location.protocol) ? "https://ssl." : "http://www.");
+document.write(unescape("%3Cscript src='" + gaJsHost + "google-analytics.com/ga.js' type='text/javascript'%3E%3C/script%3E"));
+</script>
+<script type="text/javascript">
+var pageTracker = _gat._getTracker("UA-5951066-1");
+pageTracker._trackPageview();
+</script>a
+</body>
+</html>
+
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