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author davidmurphy
date Sat, 31 Mar 2012 16:07:07 -0400
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1 <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN"
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2 "http://www.w3.org/TR/html4/transitional.dtd">
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3 <html>
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4 <head>
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5 <link rel="stylesheet" type="text/css" href="logo.css" >
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6 <title>CodonLogo - About</title>
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7 <meta name="author" content="Gavin E. Crooks" >
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8 </head>
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9
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10 <body style="align: center">
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15 <table width="80%" border = '0' cellspacing='0' cellpadding='1' align="center">
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16 <tr><td >
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17 <h1>CodonLogo 1.0</h1>
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18
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19 </td><td align = "right">
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20 &middot;
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21 <a class="selected" href="./">about</a>&nbsp;&middot;
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22 <a href="create.cgi">create</a>&nbsp;&middot;
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23 <a href="examples.html">examples</a>&nbsp;&middot;
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24 <a href="manual.html">manual</a>&nbsp;&middot;
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25 <br>
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26 <span style="font-size:small">&nbsp;</span>&nbsp;&nbsp;
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27
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28 </td></tr>
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32 <tr><td colspan="2" style="font-size:small">
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33 <a href="examples.html"><img
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34 alt="CodonLogo" width="284" height="359"
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35 src="img/Replacethis1.png" align="right" vspace="40" hspace="10"></a>
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37
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38 <h3>Introduction</h3>
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39 <p>
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40 Codonlogo is based on <a href="http://weblogo.berkeley.edu/">WebLogo</a>,a web based application designed to make the
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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.
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42 </p>
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43
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44 <p>
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45 <a href="http://www.lecb.ncifcrf.gov/~toms/sequencelogo.html">Sequence&nbsp;logos</a> are a graphical representation of an amino acid
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46 or nucleic acid multiple sequence alignment developed by
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47 <a href="http://www.lecb.ncifcrf.gov/~toms/schneider.html">Tom Schneider</a>
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48 and <a href="http://www.lecb.ncifcrf.gov/~toms/sipinfo.html">Mike
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49 Stephens</a>.
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50 Each logo consists of stacks of symbols, one stack for each position in the
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51 sequence. The overall height of the stack indicates the sequence conservation
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52 at that position, while the height of symbols within the stack indicates the
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53 relative frequency of each codon at that position. In general,
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54 a sequence logo provides a richer and more precise description of, for example,
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55 a binding site, than would a consensus sequence.
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56 </p>
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57
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58 <ul>
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59 <li><a href="create.cgi">Create your own logos </a>
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60 </li><li><a href="examples.html">View example sequence logos and input data.</a>
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61 </li><li><a href="manual.html">Read the User's Manual</a>
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62 </li><li> <a href="http://code.google.com/p/weblogo/"> Download WebLogo source code</a>
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63 </li><li> <a href="http://groups.google.com/group/WebLogo">WebLogo discussion group</a>
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64 </li>
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65 </ul>
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66
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67
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68 <h3>References</h3>
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69
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71 <p>
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72 <small>
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73 <a href="http://bespoke.lbl.gov/">Crooks GE</a>,
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74 <a href="http://compbio.berkeley.edu/">Hon G</a>,
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75 <a href="http://compbio.berkeley.edu/">Chandonia JM</a>,
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76 <a href="http://compbio.berkeley.edu/people/brenner/">Brenner SE</a>
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77 CodonLogo: A sequence logo
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78 generator, <br >
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79 <em>Genome Research</em>, 14:1188-1190, (2004)
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80 [<a href="http://bespoke.lbl.gov/pubs/fulltext/Crooks2004a-GR-WebLogo.pdf">Full Text</a> ]
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81 </small>
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82 </p>
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84 <p>
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85 <small>
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86 Schneider TD, Stephens RM. 1990.
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87 <a class="out" href="http://www.lecb.ncifcrf.gov/~toms/paper/logopaper/">Sequence Logos: A New Way to Display Consensus Sequences.</a>
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88 <em>Nucleic Acids Res.</em> <em>18</em>:6097-6100
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89 </small>
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90 </p>
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96 <h3>Disclaimer</h3>
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97
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98 <p>
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99 While no permanent records are kept of submitted sequences, we cannot
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100 undertake to guarantee that data sent to CodonLogo remains secure. Moreover,
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101 no guarantees whatsoever are provided about data generated by CodonLogo.
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102 </p>
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104
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105
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106 <h3>Feedback</h3>
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107 <p>
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108 Suggestions on how to improve CodonLogo are heartily welcomed!
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109 Please direct questions to murphy.david@gmail.com
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110 </p>
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111
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112 </td></tr>
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116 </table>
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117 <script type="text/javascript">
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118 var gaJsHost = (("https:" == document.location.protocol) ? "https://ssl." : "http://www.");
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119 document.write(unescape("%3Cscript src='" + gaJsHost + "google-analytics.com/ga.js' type='text/javascript'%3E%3C/script%3E"));
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120 </script>
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121 <script type="text/javascript">
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122 var pageTracker = _gat._getTracker("UA-5951066-1");
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123 pageTracker._trackPageview();
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124 </script>a
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125 </body>
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126 </html>
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