Mercurial > repos > davidmurphy > codonlogo

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<title>CodonLogo - About</title>
<meta name="author" content="Gavin E. Crooks" >
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<h1>CodonLogo 1.0</h1>

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    &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;

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	  <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>

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author	davidmurphy
date	Fri, 13 Jan 2012 07:18:19 -0500
parents	c55bdc2fb9fa
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