diff --git a/src/couchapp/txssdb/_attachments/index.html b/src/couchapp/txssdb/_attachments/index.html index f124d57294040041878ec9b1dfc36b2674a4fad3..c2559f45f5f3a4a74402fa08af976771f31e5214 100644 --- a/src/couchapp/txssdb/_attachments/index.html +++ b/src/couchapp/txssdb/_attachments/index.html @@ -12,117 +12,22 @@ </head> <body> -<h1>MacSyDB/TXSSdb</h1> - <div id="head"> - <p>Protein secretion systems are key virulence factors of all major bacterial pathogens with an - LPS-containing outer membrane: - <span class="species">Shigella</span>, - <span class="species">Escherichia coli</span>, - <span class="species">Yersinia pestis</span>, - <span class="species">Salmonella</span>, - <span class="species">Pseudomonas aeruginosa</span>, - <span class="species">Helicobacter pylori</span>, - <span class="species">Vibrio cholerae</span>, - etc. - Protein secretion systems are also involved in complex antagonistic ecological interactions between bacteria, - as recently exemplified by the ability of bacteria to use type 6 and type 5 - secretion systems to respond to aggressive behaviour by other bacteria. - </p> + + <img src="images/txss_mb_named.png" title="Secretion Systems schema" alt="Secretion Systems schema"> - <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 (<a href="#txsscan">TXSScan)</a>.</p> + <h1>MacSyDB/TXSSdb</h1> - <p>This database contains the results of the prediction of the most studied secretion systems in 1528 diderm bacteria: - <ul> - <li>T1SS</li> - <li>T2SS, and the related type IV pilus and Tad pilus</li> - <li>T3SS, and the related bacterial flagellum</li> - <li>T4SS </li> - <li>T5aSS, T5bSS and T5cSS</li> - <li>T6SS<span>i</span>, T6SS<span>ii</span> and T6SS<span>iii</span></li> - <li>T9SS</li> - </ul> - </p> - - <div> - <p>References:</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">(2015)</span> - <span class="citation_article_title">Identification of protein secretion systems in bacterial genomes. Submitted.</span> - <a href="http://biorxiv.org/content/early/2015/11/09/031039"> - <span class="citation_journal_title">(preprint available at http://biorxiv.org/content/early/2015/11/09/031039)</span> - </a> - </div> - <p>For T3SS and Flagellar profiles:</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>For T4SS profiles:</p> - <div class="citation"> - <span class="citation_author">Guglielmini, J.</span>, - <span class="citation_author">Quintais, L.</span>, - <span class="citation_author">Garcillan-Barcia, M. P.,</span> - <span class="citation_author">de la Cruz,F.</span> - <span class="citation_author">Rocha, E. P.</span> - <span class="citation_date">(2011)</span> - <span class="citation_article_title">The Repertoire of ICE in Prokaryotes Underscores the Unity, Diversity, and Ubiquity of Conjugation.</span></a> - <span class="citation_journal_title">PLoS Genet.</span> - <span class="citation_issue">7,</span> - <span class="citation_start_page">e1002222,</span> - <a href="https://dx.doi.org/10.1371/journal.pgen.1002222">doi:10.1371/journal.pgen.1002222</a> - </div> - <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> - </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</a> and - <a href="https://github.com/gem-pasteur/macsyview">MacSyView</a> are freely available). - 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> + <p>Protein secretion systems are key virulence factors of all major bacterial pathogens with an + LPS-containing outer membrane. They are also involved in complex antagonistic ecological interactions between + bacteria. We designed models and protein profiles to detect an unprecedented number and diversity (∼10000) + of bacterial protein secretion systems (T1SS, T2SS, T3SS, T4SS, T5SS, T6SS<sup>i-iii</sup>, T9SS) and evolutionarily related appendages + (T4P, Tad, Flagellum) in 1528 genomes of diderm bacteria. + <a href="http://macsydb.web.pasteur.fr/txssdb/_design/txssdb/index.html#txsscan">The TXSScan tool is also now available</a>. + </p> </div> <div id="request"> @@ -160,7 +65,75 @@ </fieldset> </form> </div> + <div id="results"></div> + +<div id="links"> + <p>TXSScan 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</a> and + <a href="https://github.com/gem-pasteur/macsyview">MacSyView</a> are freely available). + The documentation on these programs can be found at <a href="http://macsyfinder.readthedocs.org/">http://macsyfinder.readthedocs.org/</a>.</p> +</div> +<div id="references"> + <h2>References:</h2> + <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">(2015)</span> + <span class="citation_article_title">Identification of protein secretion systems in bacterial genomes. Submitted.</span> + <a href="http://biorxiv.org/content/early/2015/11/09/031039"> + <span class="citation_journal_title">(preprint available at http://biorxiv.org/content/early/2015/11/09/031039)</span> + </a> + </div> + <p>For T3SS and Flagellar profiles:</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>For T4SS profiles:</p> + <div class="citation"> + <span class="citation_author">Guglielmini, J.</span>, + <span class="citation_author">Quintais, L.</span>, + <span class="citation_author">Garcillan-Barcia, M. P.,</span> + <span class="citation_author">de la Cruz,F.</span> + <span class="citation_author">Rocha, E. P.</span> + <span class="citation_date">(2011)</span> + <span class="citation_article_title">The Repertoire of ICE in Prokaryotes Underscores the Unity, Diversity, and Ubiquity of Conjugation.</span></a> + <span class="citation_journal_title">PLoS Genet.</span> + <span class="citation_issue">7,</span> + <span class="citation_start_page">e1002222,</span> + <a href="https://dx.doi.org/10.1371/journal.pgen.1002222">doi:10.1371/journal.pgen.1002222</a> + </div> + <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> + </div> + +</div> + + + <div id="footer"> Visit our website: <a href="https://research.pasteur.fr/en/team/microbial-evolutionary-genomics/">Microbial evolutionary genomics group</a> diff --git a/src/couchapp/txssdb/_attachments/style/main.css b/src/couchapp/txssdb/_attachments/style/main.css index e6fa70e5663cfced4d8f32c632da201baa3a1bd9..504c150f838df0dcb54950528542904f483ef8f2 100644 --- a/src/couchapp/txssdb/_attachments/style/main.css +++ b/src/couchapp/txssdb/_attachments/style/main.css @@ -6,7 +6,7 @@ body { } h1 { - font-size:3em; + font-size:3em; text-align:center; } @@ -22,7 +22,7 @@ h2 { #head img{ display: block; margin: 0 auto; - width:80%; + width:70%; } @@ -37,6 +37,7 @@ h2 { font-size: 0.9em; #line-height: 1.8em; } + .citation_author{} .citation_date{} .citation_article_title{} @@ -76,6 +77,24 @@ h2 { #head p:first-letter{ font-weight:bold; } + +#links { + margin: 2%; +} + +#references { + margin:2%; + padding: 0.5em; + background-color: #ffffcc; + border: thin solid #cccc00; + color: black; +} + +#references p{ + margin-left:4%; + font-weight:bold; +} + #footer{ text-align:center; margin: 2em;