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    <title>Secreton</title>
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    <script src="/_utils/script/jquery.js"></script>
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  <h1>Secreton</h1>
<h2>Non-Flagellar Type III Secretion Systems in sequenced genomes</h2>
  
  <div id="head">
  
  <img src="images/systeme_complet.svg"  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., <span class="gene_name">Rhizobiales</span>).</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 Abby and Rocha 2012.</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>
  </div>
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  <div id="request">
  <form>
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			<fieldset>
				<legend>Detected NF-T3SS can be queried: </legend>
					<label for="nameSearch">by replicon name (ex:BUMA001c02)
					   <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>
						  <option value="start_with" class="ui-widget ui-corner-all ">start_with</option>
					   </select>
					   <button type="button" id="nameButton">search by name</button>
					</label>
					<label for="taxidSearch">by replicon taxon id (ex:155864) 
					   <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="famillySearch">by T3SS family 
					   <select name="familySearch" id="familyList" class="ui-widget ui-corner-all ui-state-default"> </select>
				    </label>
				    <label for="strainSearch">by strain
				        <input type="text" name="strainSearch" id="strainInput" size="100" class="ui-widget ui-corner-all" />
				    </label>
					<label for="taxonomySearch">by taxonomy
					   <input type="text" name="taxonomySearch" id="taxonomyInput" size="50" class="ui-widget ui-corner-all" />
				</label>
			</fieldset>
		</form>
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  </div>
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  <div id="results"></div>  
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  <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> 
  </div>
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  </body>
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  <script type="text/javascript">
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$(".tooltip a" , "#results").live('mouseenter', function(){
    var link$ = $(this);
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    timer = setTimeout(function(){ 
        var pos = link$.position();
        var top = pos.top + link$.outerHeight(true)+3;
        var left = pos.left + link$.outerWidth(false)-25;
        link$.next().css({top: top+"px", left: left+"px"}).show(300)}, 
        500);
    }).live( 'mouseleave', function(){
         clearTimeout(timer);
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         $(this).next().hide(300)});
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</script>
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  <script type="text/javascript">
  var get_results = function( view , args ){
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	  var url = ['_list','index',view].join('/');
	  args.limit= 45+1;
	  $("#results").load(url , $.param(args) );
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  }
  $("#nameButton").click( function(){
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	  var params = {};
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	  var $query= $("#nameQueryType").attr("value")
	  if ( $query == "start_with" ){
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		  var key= $.trim($("#nameInput").attr("value"));
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		  if( key ){ 
			  params.startkey='"'+key+'"';
			  params.endkey='"'+key+'\uFFFF"';
			  params.query_type="start_with";
		  }
	  }else{
		  var key= $("#nameInput").attr("value");
		  if( key ){ params.key='"'+key+'"'}
	  }
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	  get_results( 'by_replicon_name', params); 
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  });
  
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  $("#nameInput").keypress(function(event){
	  if(event.which == 13){
         $("#nameButton").click();
      }
  });
  
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  $("#taxidButton").click( function(){
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      var params = {};
      var key= $.trim($("#taxidInput").attr("value"));
      if( key ){ params.key = key}
      get_results( 'by_replicon_taxid', params); 
  });
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  $("#taxidInput").keypress(function(event){
      if(event.which == 13){
         $("#taxidButton").click();
      }
  });
  
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  $("#familyButton").click( function(){
      var params = {};
      var key= $.trim($("#familyInput").attr("value"));
      if( key ){ params.key='"'+key+'"'}
      get_results( 'by_family', $.param(params)); 
  });
  
  $.getJSON( "_view/t3ss_family" , {group:true}, function(response){
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	  var html = '<option value="" class="ui-widget ui-corner-all ui-widget-content">chose a T3SS Family</option>\n';
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	  for ( var i=0 ; i< response.rows.length ; i++){
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		  html = html+'<option value="'+response.rows[i].key+'" class="ui-widget ui-corner-all">'+response.rows[i].key+'</option>\n';
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	  }
	  $("#familyList").html( html );
	  $("#familyList").change(function(event){
		  var opt_value = $(event.target).val();
		  if ( opt_value){
			    var params = {};
			    params.key='"'+opt_value+'"'
			    get_results( 'by_family', params );
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		  }else{
			  $("#results div").remove();
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		  }
	  });
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  });
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  $("#strainInput").autocomplete({
	source: function(req , response){
		var term = '"'+$.trim(req.term).toLowerCase()+'"';
		var suggestions =[];
		$.getJSON("_view/strain", {key:term} , function(suggested_strain){
		      var cur_value ;
		      for(var i =0; i<suggested_strain.rows.length; i++){
		          if (cur_value != suggested_strain.rows[i].value){ 
		              suggestions.push(suggested_strain.rows[i].value);
		              cur_value = suggested_strain.rows[i].value;
		          }
		      }
		      response(suggestions);
		 });
	},
	select: function(evt , ui ){
		strain= ui.item.value ; 
		params = { key: '"'+strain+'"' };
		get_results( 'by_replicon_strain', params); 
	},
	minLength:3
  });
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  $("#strainInput").click( function (evt){
	  $("#results div").remove();
	  
  });
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  $("#strainInput").keypress(function(event){
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      if(event.which == 13){
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    	  strain= $(this).attr("value");
          params = { key: '"'+strain+'"' };
          get_results( 'by_replicon_strain', params); 
      }
  });
  
  $("#taxonomyInput").autocomplete({
	  source: function(req , response){
	        var term = '"'+req.term.toLowerCase()+'"';
	        var params= {
	        		group:true,
	        		startkey:'['+term+']',
	        		endkey:'['+term+',{}]'
	        };
	        var suggestions =[];
	        $.getJSON("_view/taxonomy_terms", params , function(suggested_term){
	              for(var i =0; i<suggested_term.rows.length; i++){
	                      suggestions.push(suggested_term.rows[i].key[1]);
	              }
	              response(suggestions);
	         });
	    },
	    select: function(evt , ui ){
	        term= ui.item.value ; 
	        params = { key: '"'+term+'"' };
	        get_results( 'by_replicon_taxonomy', params); 
	    },
	    minLength:3
	  });
  $("#taxonomyInput").click( function (evt){
      $("#results div").remove();
      
  });  
  
  $("#taxonomyInput").keypress(function(event){
      if(event.which == 13){
    	  term= $(this).attr("value");
    	  params = { key: '"'+term+'"' };
          get_results( 'by_replicon_taxonomy', params); 
      }
  });
  

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  $("#paginate .nav_page").live( 'click', function(){
	  var url = $(this).attr('data-href');
	  $("#results").load( url );
  });
  
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  $(":button").button();
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  </script>
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