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v2.3 Changes
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@HAShihab
HAShihab committed Jul 5, 2013
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7 changes: 4 additions & 3 deletions .gitignore
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# Database Configuration
*.ini
config.ini

# Server Submission(s)
*.txt
*.tab

# Benchmarking
benchmark/
# Site Verification
*1704*
sitemap*
12 changes: 10 additions & 2 deletions CHANGES.md
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Expand Up @@ -5,10 +5,18 @@ This page is a continuous listing of new features and bug fixes for the
Functional Analysis through Hidden Markov Models software and server
(http://fathmm.biocompute.org.uk).

## 5th July 2013 (v2.2)

* A new method for ranking nsSNPs according to disease concepts, i.e. disease-specific predictions, has been added.
* We now limit the number of web-based predictions shown; however, all predictions can be obtained in our tab-delimited report.
* We have fixed a number of small bugs.

* Human: updated pre-computed database to ENSEMBL 72, UniProt 2013_07, and RefSeq 59.

## 10th May 2013 (v2.2)

* We now use the Representative Proteome (RP) database when searching for homologous sequences.
* We now incorporate Pfam 27.0 into our domain-based predictions.
* Human: added support for ENSEMBL 71, UniProt 2013_05, and RefSeq 59.
* Cow: added support for ENSEMBL v71.
* We have fixed a minor database bug.

* Human: updated pre-computed database to ENSEMBL 71, UniProt 2013_05, and RefSeq 59.
214 changes: 214 additions & 0 deletions about.html
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<!DOCTYPE html>
<!--[if lt IE 7]> <html class="lt-ie9 lt-ie8 lt-ie7"> <![endif]-->
<!--[if IE 7]> <html class="lt-ie9 lt-ie8"> <![endif]-->
<!--[if IE 8]> <html class="lt-ie9"> <![endif]-->
<!--[if gt IE 8]><!--> <html class=""> <!--<![endif]-->
<head>
<title>fathmm - About Our Software and Server</title>

<meta charset="utf-8">

<meta name="viewport" content="width=device-width, initial-scale=1.0">
<meta name="description" content="About Our Software and Server">
<meta name="keywords" content="fathmm">
<meta name="author" content="Hashem A. Shihab">

<meta http-equiv="cache-control" content="max-age=0" />
<meta http-equiv="cache-control" content="no-cache" />
<meta http-equiv="expires" content="0" />
<meta http-equiv="expires" content="Tue, 01 Jan 1980 1:00:00 GMT" />
<meta http-equiv="pragma" content="no-cache" />

<link rel="icon" type="image/png" href="./img/favicon.ico">

<!-- HTML5 "Upscaling" -->
<!--[if lt IE 9]>
<script src="http://html5shiv.googlecode.com/svn/trunk/html5.js"></script>
<![endif]-->

<link href="./css/bootstrap.css" rel="stylesheet">
<link href="./css/bootstrap-responsive.css" rel="stylesheet">
<link href="./css/fathmm.css" rel="stylesheet" type="text/css">

<script type="text/javascript" src="./js/bootstrap.min.js"></script>
<script type="text/javascript" src="./js/jquery.min.js"></script>

<script type="text/javascript">
var _gaq = _gaq || [];
_gaq.push(['_setAccount', 'UA-29568329-3']);
_gaq.push(['_trackPageview']);

(function() {
var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
})();
</script>
</head>

<body>
<a id="top"></a>

<div class="container">
<div class="navbar navbar-fixed-top">
<div class="navbar-inner">
<div class="container">
<a class="btn btn-navbar" data-toggle="collapse" data-target=".nav-collapse">
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</a>
<a class="brand" href="">fathmm</a>
<div class="nav-collapse collapse">
<ul class="nav">
<li><a href="./index.html">Home</a></li>
<li><a href="./about.html">About</a></li>
<li><a href="https://github.com/HAShihab/fathmm">Download</a></li>
</ul>
<form class="navbar-form pull-right" action="./cgi-bin/results.cgi" method="post" enctype="multipart/form-data">
<input class="span3" type="text" id="session" name="session" placeholder="Enter Your Job/Session Identifier">
<button type="submit" class="btn">Fetch Results</button>
</form>
</div><!--/.nav-collapse -->
</div>
</div>
</div>

<div class="hero-unit">
<h2>About Our Software and Server</h2>
</div>


<div class="tab-content">
<div class="tab-pane active">

<div class="row">
<div class="span3" id="navparent">
<ul class="nav nav-list navex">
<li><a href="#overview"><i class="icon-chevron-right"></i> Overview</a></li>
<li><a href="#format"><i class="icon-chevron-right"></i> Input Format</a></li>
<li><a href="#format_batch"><i class="icon-chevron-right"></i> Batch Submission</a></li>
<li><a href="#vcf"><i class="icon-chevron-right"></i> Annotating VCF's</a></li>
</ul>
</div>
<div class="span9">

<section id="overview">
<h1>Overview:</h1>
<br />
<p>
The Functional Analysis through Hidden Markov Models (fathmm) software and server is is capable of <b>predicting the functional
effects of protein missense mutations</b> by combining sequence conservation within hidden Markov models (HMMs), representing the
alignment of homologous (orthologous and/or paralogous) sequences and conserved protein domains, with "pathogenicity weights", representing the overall tolerance
of the corresponding model to mutations.
<br /><br />
For more information, please refer to the following publications:
<br /><br />
Shihab HA, Gough J, Cooper DN, Stenson PD, Barker GLA, Edwards KJ, Day INM, Gaunt, TR. (2013). Predicting the Functional, Molecular and Phenotypic
Consequences of Amino Acid Substitutions using Hidden Markov Models. <i>Hum. Mutat.</i>, <b>34</b>:57-65
<a href="http://www.ncbi.nlm.nih.gov/pubmed/23033316"><img src="./img/pubmed.png" alt="fathmm - Main Paper"></a>
<br /><br />
Shihab HA, Gough J, Cooper DN, Day INM, Gaunt, TR. (2013). Predicting the Functional Consequences of Cancer-Associated Amino Acid Substitutions.
<i>Bioinformatics</i> <b>29</b>:1504-1510.
<a href="http://www.ncbi.nlm.nih.gov/pubmed/23620363"><img src="./img/pubmed.png" alt="fathmm - Cancer Paper"></a>
</p>
<br />
<a href='./about.html#top'>Back to Top ...</a>
</section>
<br />

<section id="format">
<h1>Input Format:</h1>
<br />
<p>
Our software accepts one of the following formats (see <a href="./about.html#vcf">here</a> for annotating VCF files):

<br /><br />
<ul>
<li>
<code>&lt;protein&gt; &lt;substitution&gt;</code>
</li>
<li>
<code>dbSNP rs identifiers</code>
</li>
</ul>
<br />
In the above, <code>&lt;protein&gt;</code> is the protein identifier and <code>&lt;substitution&gt;</code> is the amino acid substitution in the conventional one
letter format. At present, <b>our server accepts SwissProt/TrEMBL, RefSeq and Ensembl protein identifiers</b>, e.g.:
<br /><br />
<pre>
P43026 L441P
</pre>
or:
<br /><br />
<pre>
rs137854462
</pre>
</p>
<br />
<a href='./about.html#top'>Back to Top ...</a>
</section>
<br />

<section id="format_batch">
<h1>Batch Submission:</h1>
<br />
<p>
<b>
It is possible to submit multiple amino acid substitutions as a 'Batch Submission' via our server</b>. Here, all amino acid substitutions for a protein can be
entered on a single line and should be separated by a comma, e.g:
<br /><br />
<pre>
P43026 L441P
ENSP00000325527 N548I,E1073K,C2307S
</pre>
<br />
<b>Note: this option is not available when analysing dbSNP rs identifiers</b>.
</p>
<br />
<a href='./about.html#top'>Back to Top ...</a>
</section>
<br />

<section id="vcf">
<h1>VCF Annotation:</h1>
<br />
<p>
Unfortunately, due to disk space constraints, we are unable to annotate Variant Call Format (VCF) files on your behalf. However, the consequences of all VCF variants
can be derived using the <b><a href="http://www.ensembl.org/info/docs/variation/vep/index.html">Ensembl Variant Effect Predictor (VEP)</a></b>.
Once annotated, the following script <b><a href="./parseVCF.py">(available here)</a></b> is capable of parsing these annotations and will provide you with a list of protein
consequences which can then be used as input into our server/software.
<br /><br />
Additional help on using our script is available by typing the following command:
<br /><br />
<pre>python parseVCF.py --help</pre>
</p>
<br />
<a href='./about.html#top'>Back to Top ...</a>
</section>

</div>
</div>


</div>
</div>

<hr>
<footer>
<p>
If you have found this resource useful, please cite the following work:
<br />
<a href="http://www.ncbi.nlm.nih.gov/pubmed/23033316">Shihab HA, Gough J, Cooper DN, Stenson PD, Barker GLA, Edwards KJ, Day INM, Gaunt, TR. (2013). Predicting the Functional, Molecular and Phenotypic Consequences of Amino Acid Substitutions using Hidden Markov Models. Hum. Mutat., <b>34</b>, 57-65 </a>
</p>
<p>
We welcome any comments and/or suggestions that you may have regarding our software and server - please send an email directly to [email protected]
</p>
</footer>
</div>

<script type="text/javascript" src="./js/bootstrap.min.js"></script>
<script type="text/javascript" src="./js/jquery.min.js"></script>

</body>
</html>
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