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author davidmurphy
date Fri, 13 Jan 2012 07:18:19 -0500
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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
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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 &middot;
21 <a class="selected" href="./">about</a>&nbsp;&middot;
22 <a href="create.cgi">create</a>&nbsp;&middot;
23 <a href="examples.html">examples</a>&nbsp;&middot;
24 <a href="manual.html">manual</a>&nbsp;&middot;
25 <br>
26 <span style="font-size:small">&nbsp;</span>&nbsp;&nbsp;
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&nbsp;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
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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
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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>
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