Mercurial > repos > davidmurphy > codonlogo
comparison weblogolib/htdocs/index.html @ 7:8d676bbd1f2d
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| author | davidmurphy |
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| date | Mon, 16 Jan 2012 07:03:36 -0500 |
| parents | c55bdc2fb9fa |
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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 | |
| 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> | |
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