add paragraph about txsscan/ macsyfinder/view

src/couchapp/txssdb/_attachments/index.html

@@ -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>