Commit 38f1aace authored by Bertrand  NÉRON's avatar Bertrand NÉRON

replace search by t3ss_family by predicted system and add search by

ncbi_id
parent 100d74b5
......@@ -15,28 +15,42 @@
<h2>Non-Flagellar Type III Secretion Systems in sequenced genomes</h2>
<div id="head">
<img src="images/systeme_complet.png" title="Non-Flagellar Type III Secretion System schema" alt="Non-Flagellar Type III Secretion System schema">
<p>Non-Flagellar Type III Secretion Systems (NF-T3SS, or injectisomes) are bacterial machineries partially homologous to the bacterial flagellum,
which allow direct injection of bacterial effectors from bacterial cytoplasm to eukaryotic cells via a molecular needle (cf. schema above).
NF-T3SS are found in animal and plant pathogens (<span class="gene_name">Yersinia pestis</span>,<span class="gene_name">Escherichia coli</span>, <span class="gene_name">Burkholderia</span>,...),
but also in plant and insect symbionts (e.g., Rhizobiales).</p>
<p>This website allows to query a dataset of 216 NF-T3SS retrieved from 1385 complete genome sequences.
These systems were detected with proteic profiles of NF-T3SS core genes (<span class="gene_name">sctC</span>, <span class="gene_name">sctN</span>, <span class="gene_name">sctJ</span>,
<span class="gene_name">sctQ</span>, <span class="gene_name">sctR</span>, <span class="gene_name">sctS</span>, <span class="gene_name">sctT</span>,
<span class="gene_name">sctU</span>, <span class="gene_name">sctV</span>),
and with an analysis of the genomic context of the hits obtained.
This dataset along with the methodology is described in <a href="http://www.plosgenetics.org/doi/pgen.1002983">Abby and Rocha 2012</a>.</p>
<img src="images/systeme_complet.png" title="Non-Flagellar Type III Secretion System schema"
alt="Non-Flagellar Type III Secretion System schema">
<p>Non-Flagellar Type III Secretion Systems (NF-T3SS, or injectisomes)
are bacterial machineries partially homologous to the bacterial flagellum,
which allow direct injection of bacterial effectors from bacterial cytoplasm
to eukaryotic cells via a molecular needle (cf. schema above).
NF-T3SS are found in animal and plant pathogens
(<span class="gene_name">Yersinia pestis</span>,
<span class="gene_name">Escherichia coli</span>,
<span class="gene_name">Burkholderia</span>,...),
but also in plant and insect symbionts (e.g., Rhizobiales).</p>
<p>This website allows to query a dataset of 216 NF-T3SS retrieved from 1385 complete genome sequences.
These systems were detected with proteic profiles of NF-T3SS core genes
(<span class="gene_name">sctC</span>, <span class="gene_name">sctN</span>,
<span class="gene_name">sctJ</span>, <span class="gene_name">sctQ</span>,
<span class="gene_name">sctR</span>, <span class="gene_name">sctS</span>, <span class="gene_name">sctT</span>,
<span class="gene_name">sctU</span>, <span class="gene_name">sctV</span>),
and with an analysis of the genomic context of the hits obtained.
This dataset along with the methodology is described in
<a href="http://www.plosgenetics.org/doi/pgen.1002983">Abby and Rocha 2012</a>.</p>
<p>Proteic profiles used for this study are available to analyze user data on the
Mobyle web server: <a href="http://mobyle.pasteur.fr/cgi-bin/portal.py#forms::T3SSscan-FLAGscan" target="_blank">http://mobyle.pasteur.fr/cgi-bin/portal.py#forms::T3SSscan-FLAGscan</a>.
These profiles allow to detect both NF-T3SS and flagella.</p>
Mobyle web server:
<a href="http://mobyle.pasteur.fr/cgi-bin/portal.py#forms::T3SSscan-FLAGscan"
target="_blank">http://mobyle.pasteur.fr/cgi-bin/portal.py#forms::T3SSscan-FLAGscan</a>.
These profiles allow to detect both NF-T3SS and flagella.</p>
<div class="citation">
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>
<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>
......@@ -47,20 +61,24 @@
<fieldset>
<legend>Detected NF-T3SS can be queried: </legend>
<label for="taxidSearch">by replicon taxon id (ex:155864)
<label for="taxidSearch">by replicon 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>
<label for="ncbiidSearch">by replicon NCBI id (ex:NC_009085)
<input type="text" name="ncbiidSearch" id="ncbiidInput" class="ui-widget ui-corner-all" />
<button type="button" id="ncbiidButton">search by NCBI ID</button>
</label>
<label for="strainSearch">by strain <span style="font-size:smaller; font-style:italic;">(enter at least 3 characters)</span>
<input type="text" name="strainSearch" id="strainInput" size="100" class="ui-widget ui-corner-all" />
</label>
<label for="taxonomySearch">by taxonomy <span style="font-size:smaller; font-style:italic;">(enter at least 3 characters)</span>
<input type="text" name="taxonomySearch" id="taxonomyInput" size="50" class="ui-widget ui-corner-all" />
</label>
<label for="famillySearch">by T3SS family
<select name="familySearch" id="familyList" class="ui-widget ui-corner-all ui-state-default"> </select>
<label for="predictedSystemSearch">by Predicted system
<select name="predictedSystemSearch" id="predictedSystemList" class="ui-widget ui-corner-all ui-state-default"> </select>
</label>
<label for="nameSearch">by replicon name (ex:BUMA001c02)
<label for="nameSearch">by replicon name (ex:HADE001c01a)
<input type="text" name="nameSearch" id="nameInput"class="ui-widget ui-corner-all" />
<select name="queryType" id="nameQueryType"class="ui-widget ui-corner-all ui-state-default">
<option value="is" selected="selected" class="ui-widget ui-corner-all ">is</option>
......@@ -73,7 +91,8 @@
</div>
<div id="results"></div>
<div id="footer">
Visit our website: <a href="http://www.pasteur.fr/ip/easysite/pasteur/en/research/scientific-departments/genomes-and-genetics/units-and-groups/evolutionary-microbial-genomics/index">Microbial evolutionary genomics group</a>
Visit our website:
<a href="http://www.pasteur.fr/ip/easysite/pasteur/en/research/scientific-departments/genomes-and-genetics/units-and-groups/evolutionary-microbial-genomics/index">Microbial evolutionary genomics group</a>
</div>
</body>
<script type="text/javascript">
......@@ -130,7 +149,7 @@ $(".tooltip a" , "#results").live('mouseenter', function(){
return ;
}
}
get_results( 'by_replicon_taxid', params);
get_results( 'by_replicon_taxid', params);
});
$("#taxidInput").keypress(function(event){
......@@ -138,26 +157,48 @@ $(".tooltip a" , "#results").live('mouseenter', function(){
$("#taxidButton").click();
}
});
$("#ncbiidButton").click( function(){
var params = {};
var key= $.trim($("#ncbiidInput").attr("value"));
if( key ){
if ( /^\w{2}_(\d|\.)+$/.test( key )){
params.key='"'+key+'"';
} else{
$("#results").html( '<ul>Invalid NCBI id:'+key+'</ul>');
return ;
}
}
get_results('by_replicon_ncbi_id', params);
});
$("#ncbiidInput").keypress(function(event){
if(event.which == 13){
$("#ncbiidButton").click();
}
});
$("#familyButton").click( function(){
$("#predictedSystemButton").click( function(){
var params = {};
var key= $.trim($("#familyInput").attr("value"));
var key= $.trim($("#predictedSystemInput").attr("value"));
if( key ){ params.key='"'+key+'"'}
get_results( 'by_family', $.param(params));
get_results( 'by_predicted_system', $.param(params));
});
$.getJSON( "_view/t3ss_family" , {group:true}, function(response){
var html = '<option value="" class="ui-widget ui-corner-all ui-widget-content">choose a T3SS Family</option>\n';
$.getJSON( "_view/predicted_system" , {group:true}, function(response){
var html = '<option value="" class="ui-widget ui-corner-all ui-widget-content">choose a Predicted System</option>\n';
for ( var i=0 ; i< response.rows.length ; i++){
html = html+'<option value="'+response.rows[i].key+'" class="ui-widget ui-corner-all">'+response.rows[i].key+'</option>\n';
}
$("#familyList").html( html );
$("#familyList").change(function(event){
$("#predictedSystemList").html( html );
$("#predictedSystemList").change(function(event){
var opt_value = $(event.target).val();
if ( opt_value){
var params = {};
params.key='"'+opt_value+'"'
get_results( 'by_family', params );
get_results( 'by_predicted_system', params );
}else{
$("#results div").remove();
}
......
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment