Commit 9380aecf authored by Bertrand  NÉRON's avatar Bertrand NÉRON

add cover page for all macsydb databes

parent 120048fb
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<title>MacsyDB databases</title>
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<div id="top-header">
<a href="http://www.pasteur.fr/en" target="_blank">
<div id="iplogo"></div>
</a>
<h2 id="tagline">Pour la recherche, pour la santé, pour demain</h2>
<div id="head-pasteur"></div>
<div class="clear"></div>
<div id="image-top" class="img-filter"
style="background-image:url( https://research.pasteur.fr/wp-content/uploads/2015/06/research.pasteur.fr_genomics-1600x300.jpg)">
<h1 style="color:#eee; font-size:50px; font-weight:700; font-family:Merriweather,serif; text-align:center;
padding: 100px 0 0;">MacsyDB databases</h1>
<div id="social-links">
<a data-txt="Github" data-icon="F" class="icon hover-label" href="https://github.com/gem-pasteur"
target="_blank"></a></div>
</div>
</div>
<div id="content">
<h1>This website is the home of MacsyDB databases</h1>
<p>The information presented here was originally obtained using the MacSyFinder program (or earlier prototypes
of this program),
eventually with some subsequent curation (check the literature references below).</h1>
<p>It allows to query a dataset of protein secretion systems,
conjugative and mobilization elements, and extracellular capsules retrieved from over 2000 complete genome
sequences.</p>
<ul>
<li>Protein secretion systems: <a
href="http://macsydb.web.pasteur.fr/txssdb/_design/txssdb/index.html">TXSSdb</a></li>
<li>Non-Flagellar Type III secretion systems
(partly superseded by <a href="http://macsydb.web.pasteur.fr/txssdb/_design/txssdb/index.html">TXSSdb</a>): 
<a href="http://secreton.web.pasteur.fr/secreton/_design/secreton/index.html">Secreton</a></li>
<li>Conjugative and Mobilization systems: <a
href="http://conjdb.web.pasteur.fr/conjdb/_design/conjdb/index.html">CONJdb</a></li>
<li>Extracellular capsules: <a href="http://macsydb.web.pasteur.fr/capsuledb/_design/capsuledb/index.html">CapsuleDB</a>
</li>
</ul>
</p>
<p>The profiles and models used are freely available in our website for systematic searches in the dedicated
<a href="http://galaxy.pasteur.frGalaxy">Galaxy web server</a> (search for txsscan, conjscan, capsulefinder
tools),
or in the standalone version in conjunction with MacSyFinder and MacSyView
(MacSyFinder and  MacSyView are also freely available on <a href="https://github.com/gem-pasteur/macsyfinder">
<svg class="octicon octicon-mark-github" height="24" viewBox="0 0 16 16" width="24">
<path fill-rule="evenodd"
d="M8 0C3.58 0 0 3.58 0 8c0 3.54 2.29 6.53 5.47 7.59.4.07.55-.17.55-.38 0-.19-.01-.82-.01-1.49-2.01.37-2.53-.49-2.69-.94-.09-.23-.48-.94-.82-1.13-.28-.15-.68-.52-.01-.53.63-.01 1.08.58 1.23.82.72 1.21 1.87.87 2.33.66.07-.52.28-.87.51-1.07-1.78-.2-3.64-.89-3.64-3.95 0-.87.31-1.59.82-2.15-.08-.2-.36-1.02.08-2.12 0 0 .67-.21 2.2.82.64-.18 1.32-.27 2-.27.68 0 1.36.09 2 .27 1.53-1.04 2.2-.82 2.2-.82.44 1.1.16 1.92.08 2.12.51.56.82 1.27.82 2.15 0 3.07-1.87 3.75-3.65 3.95.29.25.54.73.54 1.48 0 1.07-.01 1.93-.01 2.2 0 .21.15.46.55.38A8.013 8.013 0 0 0 16 8c0-4.42-3.58-8-8-8z"></path>
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</a>).
The documentation on these programs can be found at <a
href="http://macsyfinder.readthedocs.org/">readthedocs</a>.
 
<p>Visit our website: <a href="https://research.pasteur.fr/en/team/microbial-evolutionary-genomics/">Microbial
evolutionary genomics group</a>.</p>
</div>
<div id="references">
<h2>References for citation purposes:</h2>
<p>Secreton:</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>
<p>ConjDB:</p>
<div class="citation">
<span class="citation_author">Guglielmini, J. et al.</span>,
<span class="citation_article_title">Key components of the eight classes of type IV secretion systems involved in bacterial conjugation or protein secretion.</span>
<span class="citation_date">(2014)</span>.
<span class="citation_journal_title"> Nucleic Acids Res.</span>,
<a href="https://dx.doi.org/10.1093/nar/gku194">doi:10.1093/nar/gku194</a>.
</div>
<p>TXSSdb:</p>
<div class="citation">
<span class="citation_author">Abby SS,</span>
<span class="citation_author">Cury J,</span>
<span class="citation_author">Guglielmini J,</span>
<span class="citation_author">Néron B,</span>
<span class="citation_author">Touchon M,</span>
<span class="citation_author">Rocha EPC.</span>
<span class="citation_date">(2016)</span>
<span class="citation_article_title">Identification of protein secretion systems in bacterial genomes.</span>
<span class="citation_journal_title">Scientific Reports</span>.
<span class="citation_issue">16;6:</span>
<span class="citation_start_page">23080</span>
<a href="https://dx.doi.org/10.1038/srep23080">doi:10.1038/srep23080</a>.
</a>
</div>
 <p>CapsuleDB:</p>
<div class="citation">
<span class="citation_author">Rendueles O,</span>
<span class="citation_author">Garcia-Garcera M,</span>
<span class="citation_author">Néron B,</span>
<span class="citation_author">Touchon M,</span>
<span class="citation_author">Rocha EP.</span> 
<span class="citation_date">(submitted)</span>
<span class="citation_article_title">Abundance and co-occurrence of extracellular capsules among Prokaryotes is epistatic and increases
environmental breadth.</span>
</div>
<div id="footer">
Visit our website:
<a href="https://research.pasteur.fr/en/team/microbial-evolutionary-genomics/">Microbial evolutionary genomics
group</a>
</div>
</div>
</body>
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