|
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
|
