Commit 08285e20 authored by Bertrand  NÉRON's avatar Bertrand NÉRON

add paragraph about txsscan/ macsyfinder/view

parent 5c7037bd
......@@ -34,7 +34,7 @@
<p>We designed models and protein profiles to detect an unprecedented number and diversity (∼10000)
of bacterial protein secretion systems and evolutionarily related appendages in partial and
complete genomic data (TXSScan, link to the bottom of the page that introduces TXSScan).</p>
complete genomic data (<a href="#txsscan">TXSScan, link to the bottom of the page that introduces TXSScan)</a>.</p>
<p>This database contains the results of the prediction of the most studied secretion systems in 1528 diderm bacteria:
<ul>
......@@ -97,6 +97,31 @@
<a href="https://dx.doi.org/10.1093/nar/gku194">doi:10.1093/nar/gku194</a>.
</div>
</div>
<div>
<p id="txsscan">The tool “TXSScan” developed and used in our study is freely available for systematic searches in large datasets (standalone version) or in a webserver.
</p>
<ul>
<li>You can use the <a href="http://mobyle.pasteur.fr/cgi-bin/portal.py#forms::txsscan">webserver version.</a></li>
<li>Or <a href="https://researchpullzone-yhello.netdna-ssl.com/wp-content/uploads/2015/10/research.pasteur.fr_txsscan-models-and-profiles-for-protein-secretion-systems.gz">
download the protein profiles and the MacSyFinder models click here: FileS1_TXSScan.tar</a>.</li>
</ul>
The models and profiles are to be used in conjunction with MacSyFinder and MacSyView
(<a href="https://github.com/gem-pasteur/macsyfinder">MacSyFinder and MacSyView are freely available</a>).
The documentation on these programs can be found at <a href="http://macsyfinder.readthedocs.org/">http://macsyfinder.readthedocs.org/</a>.</p>
<p>Reference:</p>
<div class="citation">
<span class="citation_author">Abby SS</span>,
<span class="citation_author">Rocha EPC </span>
<span class="citation_date">(2012)</span>
<a href="http://www.plosgenetics.org/doi/pgen.1002983" target="_blank">
<span class="citation_article_title">The Non-Flagellar Type III Secretion System Evolved from the Bacterial
Flagellum and Diversified into Host-Cell Adapted Systems.</span></a>
<span class="citation_journal_title">PLoS Genet</span>
<span class="citation_issue"> 8(9):</span>
<span class="citation_start_page">e1002983.</span>
</div>
</div>
</div>
<div id="request">
......@@ -104,7 +129,7 @@
<fieldset>
<legend>Detected systems can be queried: </legend>
<label for="taxidSearch">by replicon taxon id (ex:400667)
<label for="taxidSearch">by taxon id (ex:400667)
<input type="text" name="taxidSearch" id="taxidInput" class="ui-widget ui-corner-all" />
<button type="button" id="taxidButton">search by taxid</button>
</label>
......
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