Mercurial > repos > davidmurphy > codonlogo
diff weblogolib/htdocs/index.html @ 0:c55bdc2fb9fa
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| author | davidmurphy |
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| date | Thu, 27 Oct 2011 12:09:09 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/weblogolib/htdocs/index.html Thu Oct 27 12:09:09 2011 -0400 @@ -0,0 +1,135 @@ +<!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"> + · + <a class="selected" href="./">about</a> · + <a href="create.cgi">create</a> · + <a href="examples.html">examples</a> · + <a href="manual.html">manual</a> · +<br> +<span style="font-size:small"> </span> + +</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 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> + + + + + + + + +