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Commit e406e0d4 authored by Bertrand NÉRON's avatar Bertrand NÉRON
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change color gene (color.css) according to the svg schema 

add description in popup gene in genome schema
modify css to improved look of site
parent 663898c1
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Showing with 126 additions and 52 deletions
src/couchapp/secreton/_attachments/index.html
View file @ e406e0d4
......@@ -10,39 +10,59 @@
<script src="script/jquery-ui-1.8.17.custom.min.js"></script>
</head>
<body>
<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>
<div id="request">
<form>
<fieldset>
<label for="nameSearch">by replicon name (ex:BUMA001c02)</label>
<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>
</fieldset>
<fieldset>
<label for="taxidSearch">by replicon taxon id (ex:155864)</label>
<input type="text" name="taxidSearch" id="taxidInput" class="ui-widget ui-corner-all"/>
<button type="button" id="taxidButton">search by taxid</button>
</fieldset>
<fieldset>
<label for="famillySearch">by T3SS family</label>
<select name="familySearch" id="familyList" class="ui-widget ui-corner-all ui-state-default">
</select>
</fieldset>
<fieldset>
<label for="strainSearch">by strain</label>
<input type text="text" name="strainSearch" id="strainInput" size="100" class="ui-widget ui-corner-all"/>
</fieldset>
<fieldset>
<label for="taxonomySearch">by taxonomy</label>
<input type text="text" name="taxonomySearch" id="taxonomyInput" size="50" class="ui-widget ui-corner-all"/>
</fieldset>
</form>
<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>
</div>
<div id="results"></div>
</body>
<script type="text/javascript">
$(".tooltip a" , "#results").live('mouseenter', function(){
......
src/couchapp/secreton/_attachments/style/color.css
View file @ e406e0d4
.gene_sctC { background-color: BlueViolet }
.gene_sctD { background-color: Blue}
.gene_sctD2{ background-color: DarkCyan}
.gene_sctF { background-color: Cyan}
.gene_sctI { background-color: Aqua}
.gene_sctJ { background-color: DarkGreen}
.gene_sctL { background-color: Green}
.gene_sctN { background-color: ForestGreen}
.gene_sctO { background-color: LimeGreen}
.gene_sctQ { background-color: GreenYellow}
.gene_sctR { background-color: YellowGreen}
.gene_sctS { background-color: Yellow}
.gene_sctT { background-color: Gold}
.gene_sctU { background-color: GoldenRod}
.gene_sctV { background-color: Orange}
.gene_sycD { background-color: DarkOrange}
.gene_sycN { background-color: OrangeRed}
.gene_yopB { background-color: Red}
.gene_yopD { background-color: FireBrick}
.gene_yopN { background-color: Maroon}
\ No newline at end of file
.gene_SctC { background-color: #f0de2f };
.gene_SctD { background-color: #550000}
.gene_SctF { background-color: #4D4D4D}
.gene_SctI { background-color: #808080}
.gene_SctJ { background-color: #008080}
.gene_SctL { background-color: #F80E16}
.gene_SctK { background-color: #F80E16}
.gene_SctN { background-color: #F80E16}
.gene_SctO { background-color: LimeGreen}
.gene_SctQ { background-color: #0000FF}
.gene_SctR { background-color: #8800AA}
.gene_SctS { background-color: #8800AA}
.gene_SctT { background-color: #8800AA}
.gene_SctU { background-color: #8800AA}
.gene_SctV { background-color: #8800AA}
.gene_SycD { background-color: DarkGreen}
.gene_SycN { background-color: lightGreen}
.gene_YopB { background-color: #333333}
.gene_YopD { background-color: #333333}
.gene_YopN { background-color: Chartreuse}
.gene_LcrV { background-color: #333333}
src/couchapp/secreton/_attachments/style/main.css
View file @ e406e0d4
......@@ -6,7 +6,49 @@ body {
}
h1 {
margin-top:0;
font-size:3em;
text-align:center;
}
h2 {
text-align:center;
}
#head {
font:Verdana,Arial,sans-serif;
font-size: 1.1em;
}
#head img{
display: block;
margin: 0 auto;
width:400px;
}
.gene_name{
font-style:italic;
}
#request form label{
display: block;
padding: 2px;
margin: 0.5em;
}
#request form{
margin: 1em;
background-color: #F9F9F9;
}
#results{
margin-bottom:2em;
}
#head p{
text-indent:1em;
margin-right:0.5em;
margin-left:0.5em;
padding-right:0.5em;
padding-left:0.5em;
}
#head p:first-letter{
font-weight:bold;
}
\ No newline at end of file
src/couchapp/secreton/templates/secretion_system.html
View file @ e406e0d4
......@@ -2,6 +2,7 @@
<html>
<head>
<title>secretion system {{code}}</title>
<link rel="stylesheet" href="../../style/main.css" type="text/css">
<link rel="stylesheet" href="../../style/system.css" type="text/css">
<link rel="stylesheet" href="../../style/color.css" type="text/css">
<script src="/_utils/script/jquery.js" type="text/javascript"></script>
......@@ -72,6 +73,9 @@
label.push(this.text(60, 27, "match: "+gene_info.match ).attr(txt));
}
label.push(this.text(60, 42, "protein length: "+gene_info.protein_length).attr(txt));
if(gene_info.description){
label.push(this.text(60, 57, "description: "+gene_info.description).attr(txt));
}
label.hide();
popup.push( label );
var frame = this.popup( start +( (stop -start)/2 ) , 100, label , "bottom").attr({fill: "#000", stroke: "#666", "stroke-width": 2, "fill-opacity": .7});
......@@ -251,7 +255,10 @@
</head>
<body>
<h1>Type III Secretion System </h1>
<h1>Non-Flagellar Type III Secretion System</h1>
<a href="../../index.html"><img src="../../images/systeme_simple.svg" width="100px" title="Go to Secreton search page" alt="Non-Flagellar Type III Secretion System schema"></a>
<ul>
{{#replicon}}
<li>strain: {{strain}}</li>
......@@ -292,6 +299,8 @@
<th>Coverage-profile</th>
<th>Match-begin</th>
<th>Match-end</th>
<th>Gene-name</th>
<th>Description</th>
</tr>
</thead>
<tbody>
......@@ -303,7 +312,7 @@
<td>{{strand}}</td>
<td>{{begin}}</td>
<td>{{end}}</td>
<td>{{match}}</td>
<td><span class="gene_name">{{match}}</span></td>
<td>{{full_score}}</td>
<td>{{e_value}}</td>
<td>{{best_domain_score}}</td>
......@@ -312,6 +321,8 @@
<td>{{coverage_profile}}</td>
<td>{{match_begin}}</td>
<td>{{match_end}}</td>
<td>{{name}}</td>
<td>{{description}}</td>
</tr>
{{/genes}}
</tbody>
......
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