0
+ − 1 <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN"
+ − 2 "http://www.w3.org/TR/html4/transitional.dtd">
+ − 3 <html>
+ − 4 <head>
+ − 5 <link rel="stylesheet" type="text/css" href="logo.css" >
+ − 6 <title>CodonLogo - About</title>
+ − 7 <meta name="author" content="Gavin E. Crooks" >
+ − 8 </head>
+ − 9
+ − 10 <body style="align: center">
+ − 11
+ − 12
+ − 13
+ − 14
+ − 15 <table width="80%" border = '0' cellspacing='0' cellpadding='1' align="center">
+ − 16 <tr><td >
+ − 17 <h1>CodonLogo 1.0</h1>
+ − 18
+ − 19 </td><td align = "right">
+ − 20 ·
+ − 21 <a class="selected" href="./">about</a> ·
+ − 22 <a href="create.cgi">create</a> ·
+ − 23 <a href="examples.html">examples</a> ·
+ − 24 <a href="manual.html">manual</a> ·
+ − 25 <br>
+ − 26 <span style="font-size:small"> </span>
+ − 27
+ − 28 </td></tr>
+ − 29
+ − 30
+ − 31
+ − 32 <tr><td colspan="2" style="font-size:small">
+ − 33 <a href="examples.html"><img
+ − 34 alt="CodonLogo" width="284" height="359"
+ − 35 src="img/Replacethis1.png" align="right" vspace="40" hspace="10"></a>
+ − 36
+ − 37
+ − 38 <h3>Introduction</h3>
+ − 39 <p>
+ − 40 Codonlogo is based on <a href="http://weblogo.berkeley.edu/">WebLogo</a>,a web based application designed to make the
+ − 41 generation of sequence logos easy and painless.CodonLogo Extends Weblogo to allow generation of sequence logos with codons rather than amino acids or nucleotides.
+ − 42 </p>
+ − 43
+ − 44 <p>
+ − 45 <a href="http://www.lecb.ncifcrf.gov/~toms/sequencelogo.html">Sequence logos</a> are a graphical representation of an amino acid
+ − 46 or nucleic acid multiple sequence alignment developed by
+ − 47 <a href="http://www.lecb.ncifcrf.gov/~toms/schneider.html">Tom Schneider</a>
+ − 48 and <a href="http://www.lecb.ncifcrf.gov/~toms/sipinfo.html">Mike
+ − 49 Stephens</a>.
+ − 50 Each logo consists of stacks of symbols, one stack for each position in the
+ − 51 sequence. The overall height of the stack indicates the sequence conservation
+ − 52 at that position, while the height of symbols within the stack indicates the
+ − 53 relative frequency of each codon at that position. In general,
+ − 54 a sequence logo provides a richer and more precise description of, for example,
+ − 55 a binding site, than would a consensus sequence.
+ − 56 </p>
+ − 57
+ − 58 <ul>
+ − 59 <li><a href="create.cgi">Create your own logos </a>
+ − 60 </li><li><a href="examples.html">View example sequence logos and input data.</a>
+ − 61 </li><li><a href="manual.html">Read the User's Manual</a>
+ − 62 </li><li> <a href="http://code.google.com/p/weblogo/"> Download WebLogo source code</a>
+ − 63 </li><li> <a href="http://groups.google.com/group/WebLogo">WebLogo discussion group</a>
+ − 64 </li>
+ − 65 </ul>
+ − 66
+ − 67
+ − 68 <h3>References</h3>
+ − 69
+ − 70
+ − 71 <p>
+ − 72 <small>
+ − 73 <a href="http://bespoke.lbl.gov/">Crooks GE</a>,
+ − 74 <a href="http://compbio.berkeley.edu/">Hon G</a>,
+ − 75 <a href="http://compbio.berkeley.edu/">Chandonia JM</a>,
+ − 76 <a href="http://compbio.berkeley.edu/people/brenner/">Brenner SE</a>
+ − 77 CodonLogo: A sequence logo
+ − 78 generator, <br >
+ − 79 <em>Genome Research</em>, 14:1188-1190, (2004)
+ − 80 [<a href="http://bespoke.lbl.gov/pubs/fulltext/Crooks2004a-GR-WebLogo.pdf">Full Text</a> ]
+ − 81 </small>
+ − 82 </p>
+ − 83
+ − 84 <p>
+ − 85 <small>
+ − 86 Schneider TD, Stephens RM. 1990.
+ − 87 <a class="out" href="http://www.lecb.ncifcrf.gov/~toms/paper/logopaper/">Sequence Logos: A New Way to Display Consensus Sequences.</a>
+ − 88 <em>Nucleic Acids Res.</em> <em>18</em>:6097-6100
+ − 89 </small>
+ − 90 </p>
+ − 91
+ − 92
+ − 93
+ − 94
+ − 95
+ − 96 <h3>Disclaimer</h3>
+ − 97
+ − 98 <p>
+ − 99 While no permanent records are kept of submitted sequences, we cannot
+ − 100 undertake to guarantee that data sent to CodonLogo remains secure. Moreover,
+ − 101 no guarantees whatsoever are provided about data generated by CodonLogo.
+ − 102 </p>
+ − 103
+ − 104
+ − 105
+ − 106 <h3>Feedback</h3>
+ − 107 <p>
+ − 108 Suggestions on how to improve CodonLogo are heartily welcomed!
+ − 109 Please direct questions to murphy.david@gmail.com
+ − 110 </p>
+ − 111
+ − 112 </td></tr>
+ − 113
+ − 114
+ − 115
+ − 116 </table>
+ − 117 <script type="text/javascript">
+ − 118 var gaJsHost = (("https:" == document.location.protocol) ? "https://ssl." : "http://www.");
+ − 119 document.write(unescape("%3Cscript src='" + gaJsHost + "google-analytics.com/ga.js' type='text/javascript'%3E%3C/script%3E"));
+ − 120 </script>
+ − 121 <script type="text/javascript">
+ − 122 var pageTracker = _gat._getTracker("UA-5951066-1");
+ − 123 pageTracker._trackPageview();
+ − 124 </script>a
+ − 125 </body>
+ − 126 </html>
+ − 127
+ − 128
+ − 129
+ − 130
+ − 131
+ − 132
+ − 133
+ − 134
+ − 135
