Team:Amsterdam/maarten/

From 2012.igem.org

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 +
{{Team:Amsterdam/toolStyleBase}}
 +
{{Team:Amsterdam/toolStyleSunburst}}
 +
{{Team:Amsterdam/stylesheet}}
 +
{{Team:Amsterdam/scripts}}
 +
{{Team:Amsterdam/Header}}
 +
{{Team:Amsterdam/Sidebar2}}
<html>
<html>
-
<head>
+
<script type='text/javascript' src='/Team:Amsterdam/maarten/slides.min.jquery.js?action=raw'></script>
-
<script src="//ajax.googleapis.com/ajax/libs/jquery/1.8.0/jquery.min.js"></script>
+
-
<script type='text/javascript'>
+
-
 
+
-
(function() {
+
-
  var ua = navigator.userAgent,
+
-
      iStuff = ua.match(/iPhone/i) || ua.match(/iPad/i),
+
-
      typeOfCanvas = typeof HTMLCanvasElement,
+
-
      nativeCanvasSupport = (typeOfCanvas == 'object' || typeOfCanvas == 'function'),
+
-
      textSupport = nativeCanvasSupport
+
-
        && (typeof document.createElement('canvas').getContext('2d').fillText == 'function');
+
-
  //I'm setting this based on the fact that ExCanvas provides text support for IE
+
-
  //and that as of today iPhone/iPad current text support is lame
+
-
  labelType = (!nativeCanvasSupport || (textSupport && !iStuff))? 'Native' : 'HTML';
+
-
  nativeTextSupport = labelType == 'Native';
+
-
  useGradients = nativeCanvasSupport;
+
-
  animate = !(iStuff || !nativeCanvasSupport);
+
-
})();
+
-
 
+
-
var Log = {
+
-
  elem: false,
+
-
  write: function(text){
+
-
    if (!this.elem)
+
-
      this.elem = document.getElementById('log');
+
-
    this.elem.innerHTML = text;
+
-
    this.elem.style.left = (500 - this.elem.offsetWidth / 2) + 'px';
+
-
  }
+
-
};
+
-
 
+
-
function visualization(number){
+
-
$('#infovis').empty()
+
-
json = JSON.parse(unescape($(':input[name=json'+number+']').val()))
+
-
    //init data
+
-
    //init Sunburst
+
-
    var sb = new $jit.Sunburst({
+
-
        //id container for the visualization
+
-
        injectInto: 'infovis',
+
-
        //Distance between levels
+
-
        levelDistance: 90,
+
-
        //Change node and edge styles such as
+
-
        //color, width and dimensions.
+
-
        Node: {
+
-
          overridable: true,
+
-
          type: useGradients? 'gradient-multipie' : 'multipie'
+
-
        },
+
-
        //Select canvas labels
+
-
        //'HTML', 'SVG' and 'Native' are possible options
+
-
        Label: {
+
-
          type: labelType
+
-
        },
+
-
        //Change styles when hovering and clicking nodes
+
-
        NodeStyles: {
+
-
          enable: true,
+
-
          type: 'Native',
+
-
          stylesClick: {
+
-
            'color': '#000000'
+
-
          },
+
-
        },
+
-
        //Add tooltips
+
-
        Tips: {
+
-
          enable: true,
+
-
          onShow: function(tip, node) {
+
-
            var html = "<div class=\"tip-title\">" + node.data.description + "</div>";
+
-
            var data = node.data;
+
-
            if("length" in data) {
+
-
              html += "<b>Length of feature:</b> " + data.length + "bp";
+
-
            }
+
-
if("type" in data){
+
-
html += "<br\><b>Type of feature:</b> " + data.type;
+
-
}
+
-
            tip.innerHTML = html;
+
-
          }
+
-
        },
+
-
        //implement event handlers
+
-
        Events: {
+
-
          enable: true,
+
-
          onClick: function(node) {
+
-
            if(!node) return;
+
-
            //Build detailed information about the file/folder
+
-
            //and place it in the right column.
+
-
            var html = "<h4>" + node.name + "</h4>", data = node.data;
+
-
            if("dna" in data) {
+
-
              html += "<br /><br /><b>Sequence:</b><br /><pre>" + data.dna + "</pre>";
+
-
            }
+
-
            $jit.id('inner-details').innerHTML = html;
+
-
            //hide tip
+
-
            sb.tips.hide();
+
-
            //rotate
+
-
            //sb.rotate(node, animate? 'animate' : 'replot', {
+
-
              //duration: 1000,
+
-
              //transition: $jit.Trans.Quart.easeInOut
+
-
            //});
+
-
          }
+
-
        },
+
-
        // Only used when Label type is 'HTML' or 'SVG'
+
-
        // Add text to the labels.
+
-
        // This method is only triggered on label creation
+
-
        onCreateLabel: function(domElement, node){
+
-
          var labels = sb.config.Label.type,
+
-
              aw = node.getData('length');
+
-
          if (labels === 'HTML' && (node._depth < 2 || aw > 2000)) {
+
-
            domElement.innerHTML = node.name;
+
-
          } else if (labels === 'SVG' && (node._depth < 2 || aw > 2000)) {
+
-
            domElement.firstChild.appendChild(document.createTextNode(node.name));
+
-
          }
+
-
        },
+
-
        // Only used when Label type is 'HTML' or 'SVG'
+
-
        // Change node styles when labels are placed
+
-
        // or moved.
+
-
        onPlaceLabel: function(domElement, node){
+
-
          var labels = sb.config.Label.type;
+
-
          if (labels === 'SVG') {
+
-
            var fch = domElement.firstChild;
+
-
            var style = fch.style;
+
-
            style.display = '';
+
-
            style.cursor = 'pointer';
+
-
            style.fontSize = "0.8em";
+
-
            fch.setAttribute('fill', "#fff");
+
-
          } else if (labels === 'HTML') {
+
-
            var style = domElement.style;
+
-
            style.display = '';
+
-
            style.cursor = 'pointer';
+
-
            style.fontSize = "0.8em";
+
-
            style.color = "#ddd";
+
-
            var left = parseInt(style.left);
+
-
            var w = domElement.offsetWidth;
+
-
            style.left = (left - w / 2) + 'px';
+
-
          }
+
-
        }
+
-
  });
+
-
    //load JSON data.
+
-
    sb.loadJSON(json);
+
-
    //compute positions and plot.
+
-
    sb.refresh();
+
-
+
-
    //end
+
-
}
+
-
 
+
-
function addForbiddenSequences(){
+
-
forbiddenSequences.addSite('Forbidden-EcoRI','GAATTC')
+
-
forbiddenSequences.addSite('Forbidden-XbaI','GAATTC')
+
-
forbiddenSequences.addSite('Forbidden-SpeI','ACTAGT')
+
-
forbiddenSequences.addSite('Forbidden-PstI','CTGCAG')
+
-
forbiddenSequences.addSite('Forbidden-NotI','GCGGCCGC')
+
-
}
+
-
 
+
-
var forbiddenSequences = {
+
-
    forbiddenSequencesArray : {},
+
-
addSite : function(name,sequence){
+
-
forbiddenSequences.forbiddenSequencesArray[name] = sequence
+
-
},
+
-
}
+
-
 
+
-
function checkOccurrence(target,sequence){
+
-
if (sequence.length > target.length){
+
-
        if (sequence.indexOf(target) == -1){
+
-
            return false
+
-
        } else{
+
-
            return true
+
-
        }
+
-
} else{
+
-
if (target.indexOf(sequence) == -1){
+
-
            return false
+
-
        } else{
+
-
            return true
+
-
        }
+
-
}
+
-
}
+
-
 
+
-
function randomDNA(length){
+
-
chars = 'atgc'
+
-
inForbiddenSite = true
+
-
while (inForbiddenSite === true){
+
-
sequence = ''
+
-
inForbiddenSite = false
+
-
for (k=0; k<length; k++) {
+
-
rnum = Math.floor(Math.random() * chars.length);
+
-
sequence += chars.substring(rnum,rnum+1);
+
-
}
+
-
for (item in forbiddenSequences.forbiddenSequencesArray){
+
-
if (checkOccurrence(sequence,forbiddenSequences.forbiddenSequencesArray[item].toLowerCase()) === false){
+
-
continue
+
-
} else{
+
-
inForbiddenSite = true
+
-
break
+
-
}
+
-
}
+
-
}
+
-
return sequence
+
-
}
+
-
 
+
-
function getMethyltransferases(){
+
-
    methyltransferases = new Array()
+
-
    sca1 = new Object()
+
-
    sca1.target = "AGTACT"
+
-
    sca1.sequence = "tccgggcgggactttggatatgtgatacagtcgtccgctgcactatggaatcgactctctacattctcacagagaggaaaagccttggacaccaggcttgcagacatcaagaaggccctggggaagccgtactacgaaacctcggatgtccttctttaccacggcgacagtcttgagctgctcaagtcaatgcctcagcagattttcgaccttaccgtaactagcccaccttacaatattggcaaagagtacgagggtgtactgtcgatcgaggaatacatttcctggtgcgagacatggatgtcgcgcgttcatagggcgaccagcgcaggcggcgcattttggctcaatgttgggtacgtccctgtcccgaaccaaggaaaagcagtcccgattccttacctcttgtgggacaagagtccgttctacatgatccaggaagttgtctggaattacggggcgggagtggcgtctcgaaaatcgttttccccgcgcaatgaaaagtttctctggtatgtgcgcgacccgctgaattattacttcgacctcgattcggtgcgcgacccaaatgtgaaataccccaaccagaaaaagaatgggaagctcaaatgcaacccgttggggaaaaatcccactgacgtttggcagttccccaaggttacgtcgggcgcgaagagatcaagcgtggagcgcaccgcccatccggcacaattcccgtctgctgtcattgaacgggtcatcaaggcgtgcagcccttccgacggcgtcatcctggacccattcctcggttccggaacgacctcgctgaccgccagaaagcaaggccggtgcagcgtcggtatcgaaatccgcgaagactacctcgacatcgcggtgggacgcctggaggcggaggcgcaatccctcttctag"
+
-
    sca1.description = "M.Sca1"
+
-
sca2 = new Object()
+
-
sca2.target = "AGTACC"
+
-
sca2.sequence = "tccgggcgggactttggatatgtgatacagtcgtccgctgcactatggaatcgactctctacattctcacagagaggaaaagccttggacaccaggcttgcagacatcaagaaggccctggggaagccgtactacgaaacctcggatgtccttctttaccacggcgacagtcttgagctgctcaagtcaatgcctcagcagattttcgaccttaccgtaactagcccaccttacaatattggcaaagagtacgagggtgtactgtcgatcgaggaatacatttcctggtgcgagacatggatgtcgcgcgttcatagggcgaccagcgcaggcggcgcattttggctcaatgttgggtacgtccctgtcccgaaccaaggaaaagcagtcccgattccttacctcttgtgggacaagagtccgttctacatgatccaggaagttgtctggaattacggggcgggagtggcgtctcgaaaatcgttttccccgcgcaatgaaaagtttctctggtatgtgcgcgacccgctgaattattacttcgacctcgattcggtgcgcgacccaaatgtgaaataccccaaccagaaaaagaatgggaagctcaaatgcaacccgttggggaaaaatcccactgacgtttggcagttccccaaggttacgtcgggcgcgaagagatcaagcgtggagcgcaccgcccatccggcacaattcccgtctgctgtcattgaacgggtcatcaaggcgtgcagcccttccgacggcgtcatcctggacccattcctcggttccggaacgacctcgctgaccgccagaaagcaaggccggtgcagcgtcggtatcgaaatccgcgaagactacctcgacatcgcggtgggacgcctggaggcggaggcgcaatccctcttctagg"
+
-
    sca2.description = "M.Sca2"
+
-
methyltransferases[0] = sca1
+
-
methyltransferases[1] = sca2
+
-
addForbiddenSequence(methyltransferases,'hasTarget')
+
-
    return methyltransferases
+
-
}
+
-
 
+
-
function getZincFingers(){
+
-
    zincFingers = new Array()
+
-
    rawData = document.plasmidForm.zf.value
+
-
    rawData = rawData.split('>')
+
-
    rawData.reverse().pop()
+
-
    rawData.reverse()
+
-
    for (zf in rawData){
+
-
        zfFormatted = rawData[zf].split('\n')
+
-
        zfDescription = zfFormatted[0]
+
-
        zfTarget = zfDescription.split('|')[5]
+
-
        zfSequence = ''
+
-
        for (i=1;i<zfFormatted.length;i++){
+
-
            zfSequence+=zfFormatted[i]
+
-
        }
+
-
        zfObject = new Object()
+
-
        zfObject.target = zfTarget
+
-
        zfObject.sequence = zfSequence
+
-
        zfObject.description = zfDescription
+
-
        zincFingers[zf] = zfObject
+
-
    }
+
-
    addForbiddenSequence(zincFingers,'hasTarget')
+
-
    return zincFingers
+
-
}
+
-
 
+
-
function getLinkers(){
+
-
    linkers = new Array()
+
-
    linker1 = new Object()
+
-
    linker1.sequence = "gcacccggc"
+
-
    linker1.description = "Linker 1"
+
-
linker2 = new Object()
+
-
linker2.sequence = "gcaccccgccc"
+
-
linker2.description = "Linker 2"
+
-
    linkers[0] = linker1
+
-
linkers[1] = linker2
+
-
addForbiddenSequence(linkers,'noTarget')
+
-
    return linkers
+
-
}
+
-
 
+
-
function getMycTags(){
+
-
    mycTags = new Array()
+
-
    mycTag1 = new Object()
+
-
    mycTag1.sequence = "gaacagaaactcatctctgaagaggatctg"
+
-
    mycTag1.description = "Myc Tag 1"
+
-
mycTag2 = new Object()
+
-
mycTag2.sequence = "gaacagaaactcatctctgaagagaatctgaagactgagtcagt"
+
-
mycTag2.description = "Myc Tag 2"
+
-
    mycTags[0] = mycTag1
+
-
mycTags[1] = mycTag2
+
-
addForbiddenSequence(mycTags,'noTarget')
+
-
    return mycTags
+
-
}
+
-
 
+
-
function getTerminators(){
+
-
    terminators = new Array()
+
-
    terminator1 = new Object()
+
-
    terminator1.sequence = "tcacactggctcaccttcgggtgggcctttctgcgtttatatactagagagagaatataaaaagccagattattaatccggcttttttattattt"
+
-
    terminator1.description = "B0014 containing BOO12 and BOO11 terminators"
+
-
terminator2 = new Object()
+
-
terminator2.sequence = "tcacactggctcaccttcgggtgggcctttctgcgtttatatactagagagagaatataaaaagccagattattaatccggcttttttattatttt"
+
-
    terminator2.description = "Terminator 2"
+
-
terminators[0] = terminator1
+
-
terminators[1] = terminator2
+
-
addForbiddenSequence(terminators,'noTarget')
+
-
    return terminators
+
-
}
+
-
 
+
-
function getRBS(){
+
-
    rbs = new Array()
+
-
    rbs1 = new Object()
+
-
    rbs1.sequence = "tcacacaggaaag"
+
-
    rbs1.description = "BBa_B0032"
+
-
    rbs2 = new Object()
+
-
    rbs2.sequence = "aaaaaaaaaaaccccaa"
+
-
    rbs2.description = "RBS2"
+
-
    rbs[0] = rbs1
+
-
    rbs[1] = rbs2
+
-
addForbiddenSequence(rbs,'noTarget')
+
-
    return rbs
+
-
}
+
-
 
+
-
function addForbiddenSequence(array,type){
+
-
if (type == 'hasTarget'){
+
-
for (item in array){
+
-
forbiddenSequences.addSite(array[item].description,array[item].target)
+
-
}
+
-
} else{
+
-
for (item in array){
+
-
forbiddenSequences.addSite(array[item].description,array[item].sequence)
+
-
}
+
-
}
+
-
+
-
}
+
-
 
+
-
function getDate(){
+
-
    today = new Date()
+
-
    dd = today.getDate()
+
-
    mm = today.getMonth()+1
+
-
    yyyy = today.getFullYear()
+
-
    if(dd<10){
+
-
        dd='0'+dd
+
-
    }
+
-
    if(mm<10){
+
-
        mm='0'+mm
+
-
    }
+
-
    today = dd+'-'+mm.substring(0,2)+'-'+yyyy;
+
-
    return today
+
-
}
+
-
 
+
-
function generateWhiteSpace(amount){
+
-
        output = ''
+
-
        for (i=0;i<amount;i++){
+
-
            output += '&nbsp;'
+
-
        }
+
-
        return output
+
-
}
+
-
 
+
-
function staticGenbank(name){
+
-
output = 'LOCUS'
+
-
        output += generateWhiteSpace(16)
+
-
        output += name
+
-
        output += generateWhiteSpace(8)
+
-
        output += memoryPlasmid.dna.length+' bp DNA '
+
-
        output += generateWhiteSpace(3)
+
-
        output += 'linear'
+
-
        output += generateWhiteSpace(7)
+
-
        output += getDate()+'<br>'
+
-
        output += 'DEFINITION<br>'
+
-
        output += 'ACCESSION<br>'
+
-
        output += 'VERSION<br>'
+
-
        output += 'SOURCE<br>'
+
-
        output += ' &nbsp;ORGANISM<br>'
+
-
        output += 'COMMENT<br>'
+
-
        output += 'FEATURES'
+
-
        output += generateWhiteSpace(13)
+
-
        output += 'Location/Qualifiers<br>'
+
-
return output
+
-
}
+
-
 
+
-
function genbankRestriction(targetSites){
+
-
restrictionPlasmidOutput = staticGenbank('restriction_plasmid')
+
-
restrictionOrigin = memoryPlasmid.features[1].sequence
+
-
for (key in targetSites){
+
-
    restrictionOrigin += randomDNA(10)
+
-
    restrictionPlasmidOutput += generateWhiteSpace(5)
+
-
restrictionPlasmidOutput += 'misc_feature'
+
-
restrictionPlasmidOutput += generateWhiteSpace(5)
+
-
restrictionPlasmidOutput += restrictionOrigin.length+1+'...'
+
-
    restrictionOrigin += targetSites[key].zincFinger
+
-
restrictionPlasmidOutput += restrictionOrigin.length+'<br>'
+
-
restrictionOrigin += randomDNA(10)
+
-
restrictionPlasmidOutput += generateWhiteSpace(5)
+
-
restrictionPlasmidOutput += 'misc_feature'
+
-
restrictionPlasmidOutput += generateWhiteSpace(5)
+
-
restrictionPlasmidOutput += restrictionOrigin.length+1+'...'
+
-
    restrictionOrigin += targetSites[key].methyltransferase
+
-
restrictionPlasmidOutput += restrictionOrigin.length+'<br>'
+
-
restrictionOrigin += targetSites[key].methyltransferase
+
-
}
+
-
restrictionOrigin = restrictionOrigin.toLowerCase()
+
-
        restrictionOrigin = restrictionOrigin.replace(/[atgc]{10}/g,'$& ').replace(/amp;/g,'').split(' ')
+
-
        pos = 1
+
-
        newString = ''
+
-
        restrictionPlasmidOutput += 'ORIGIN<br>'
+
-
        for (i=0;i<restrictionOrigin.length;i++){
+
-
            newString = newString+' '+restrictionOrigin[i]
+
-
            if ((i+1)%6===0){
+
-
                whiteSpace = ''
+
-
                for (j=0;j<9-pos.toString().length;j++){
+
-
                    whiteSpace+= '&nbsp;'
+
-
                }
+
-
                newString = whiteSpace+pos + ' ' + newString
+
-
                restrictionPlasmidOutput+=newString+'<br>'
+
-
                newString = ''
+
-
            } else if ((i+1)%6==1){
+
-
                  if (i!=0){
+
-
                      pos+=60
+
-
                  }
+
-
              }
+
-
        }
+
-
        if (restrictionOrigin.length%6 != 0){
+
-
            newString = ''
+
-
            whiteSpace = ''
+
-
            for (j=0;j<9-pos.toString().length;j++){
+
-
                whiteSpace+= '&nbsp;'
+
-
            }
+
-
            newString+=whiteSpace+pos
+
-
            for (i=0;i<(restrictionOrigin.length%6);i++){
+
-
                newString+=' '+restrictionOrigin[restrictionOrigin.length-restrictionOrigin.length%6+i]
+
-
            }
+
-
            restrictionPlasmidOutput+=newString+'<br>'
+
-
        }
+
-
restrictionSiteWindow = window.open()
+
-
restrictionSiteWindow.document.write(restrictionPlasmidOutput)
+
-
restrictionSiteWindow.focus()
+
-
}
+
-
function genbankMemory(){
+
-
        memoryPlasmidOutput = staticGenbank('memory_plasmid')
+
-
        for (item in memoryPlasmid.memoryObjects){
+
-
    for (key in memoryPlasmid.memoryObjects[item]){
+
-
memoryPlasmidOutput += generateWhiteSpace(5)
+
-
memoryPlasmidOutput += 'misc_feature'
+
-
memoryPlasmidOutput += generateWhiteSpace(5)
+
-
memoryPlasmidOutput += memoryPlasmid.memoryObjects[item][key].start+'...'+memoryPlasmid.memoryObjects[item][key].end+'<br>'
+
-
memoryPlasmidOutput += generateWhiteSpace(10)
+
-
memoryPlasmidOutput += '/label='+memoryPlasmid.memoryObjects[item][key].description+'<br>'
+
-
}
+
-
           
+
-
        }
+
-
        origin = memoryPlasmid.dna
+
-
        origin = origin.replace(/[atgc]{10}/g,'$& ').replace(/amp;/g,'').split(' ')
+
-
        pos = 1
+
-
        newString = ''
+
-
        memoryPlasmidOutput += 'ORIGIN<br>'
+
-
        for (i=0;i<origin.length;i++){
+
-
            newString = newString+' '+origin[i]
+
-
            if ((i+1)%6===0){
+
-
                whiteSpace = ''
+
-
                for (j=0;j<9-pos.toString().length;j++){
+
-
                    whiteSpace+= '&nbsp;'
+
-
                }
+
-
                newString = whiteSpace+pos + ' ' + newString
+
-
                memoryPlasmidOutput+=newString+'<br>'
+
-
                newString = ''
+
-
            } else if ((i+1)%6==1){
+
-
                  if (i!=0){
+
-
                      pos+=60
+
-
                  }
+
-
              }
+
-
        }
+
-
        if (origin.length%6 != 0){
+
-
            newString = ''
+
-
            whiteSpace = ''
+
-
            for (j=0;j<9-pos.toString().length;j++){
+
-
                whiteSpace+= '&nbsp;'
+
-
            }
+
-
            newString+=whiteSpace+pos
+
-
            for (i=0;i<(origin.length%6);i++){
+
-
                newString+=' '+origin[origin.length-origin.length%6+i]
+
-
            }
+
-
            memoryPlasmidOutput+=newString+'<br>'
+
-
        }
+
-
+
-
        myWindow=window.open()
+
-
        myWindow.document.write(memoryPlasmidOutput)
+
-
        myWindow.focus()
+
-
+
-
}
+
-
 
+
-
function formatPlasmidInput(backbone){
+
-
        backbone = backbone.split('\n')
+
-
        originBoolean = false
+
-
        backboneName = ''
+
-
        sequence = ''
+
-
        if (backbone[0].toLowerCase().indexOf('locus') != -1){
+
-
            for (i=0;i<backbone.length;i++){
+
-
                if (originBoolean === true){
+
-
                    if (backbone[i].indexOf('//') == -1){
+
-
                      appendThis = backbone[i].replace(/[0-9]|\s|\n|\t/g,'')
+
-
                      sequence = sequence+appendThis
+
-
                    } else{
+
-
                        originalBoolean = false
+
-
                    }
+
-
                }
+
-
                if (backbone[i].indexOf('locus') != -1){
+
-
                    backboneName = backbone[i].split(/\s+|\t+/g)[1]
+
-
                }
+
-
                if (backbone[i].indexOf('origin') != -1){
+
-
                    originBoolean = true
+
-
                }
+
-
            }
+
-
        } else if (backbone[0][0] == '>'){
+
-
                for (i=0;i<backbone.length;i++){
+
-
                    if (backbone[i][0] != '>'){
+
-
                        appendThis = backbone[i].replace(/[0-9]|\s|\n|\t/g,'')
+
-
                        sequence = sequence+appendThis
+
-
                    } else{
+
-
                        backboneName = backbone[i].replace('>','')
+
-
                    }
+
-
                }
+
-
        }
+
-
        memoryPlasmid.addFeature(1,sequence.length,'Backbone',sequence,backboneName,'')
+
-
        return sequence
+
-
}
+
-
 
+
-
function feature(start,end,type,sequence,description,featureObject){
+
-
this.start = start;
+
-
this.end = end;
+
-
this.type = type;
+
-
    this.sequence = sequence;
+
-
    this.description = description;
+
-
this.featureObject = featureObject
+
-
}
+
-
 
+
-
var restrictionPlasmid = {
+
-
backboneName : '',
+
-
dna : '',
+
-
features : {},
+
-
    setBackboneName : function(backboneName){
+
-
        restrictionlasmid.backboneName = backboneName
+
-
    },
+
-
setDNA : function(dna){
+
-
restrictionPlasmid.dna = dna
+
-
},
+
-
addFeature : function(start,end,type,sequence,description){
+
-
restrictionPlasmid.features[start] = new feature(start,end,type,sequence,description)
+
-
},
+
-
addRecognitionAreaObject : function(zfTarget,mtaseTarget){
+
-
 
+
-
recognitionPlasmid.zfTarget = zfTarget
+
-
recognitionPlasmid.mtaseTarget = mtaseTarget
+
-
}
+
-
}
+
-
 
+
-
var memoryPlasmid = {
+
-
    backboneName : '',
+
-
dna : '',
+
-
features : {},
+
-
memoryObjects : {},
+
-
    setBackboneName : function(backboneName){
+
-
        memoryPlasmid.backboneName = backboneName
+
-
    },
+
-
setDNA : function(dna){
+
-
memoryPlasmid.dna = dna
+
-
},
+
-
addMemoryObject : function(sensor,rbs,zincFinger,linker,mycTag,methyltransferase,terminator){
+
-
memoryObject = new Object()
+
-
memoryObject.sensor = sensor
+
-
memoryObject.rbs = rbs
+
-
memoryObject.zincFinger = zincFinger
+
-
memoryObject.linker = linker
+
-
memoryObject.mycTag = mycTag
+
-
memoryObject.methyltransferase = methyltransferase
+
-
memoryObject.terminator = terminator
+
-
    memoryPlasmid.memoryObjects[sensor.start] = memoryObject
+
-
},
+
-
addFeature : function(start,end,type,sequence,description){
+
-
memoryPlasmid.features[start] = new feature(start,end,type,sequence,description)
+
-
}
+
-
}
+
-
 
+
-
function sensorObject(name,sequence){
+
-
        this.name = name
+
-
        this.sequence = sequence
+
-
+
-
}
+
-
     
+
-
function formatSensors(sensors){
+
-
        sensorArray = new Array()
+
-
        if (sensors.indexOf('LOCUS') != -1){
+
-
            sensors = sensors.split('LOCUS')
+
-
            sensors.reverse().pop()
+
-
            for (i=0;i<sensors.length;i++){
+
-
                originBoolean = false
+
-
                sensorName = ''
+
-
                sequence = ''
+
-
                sensor = sensors[i].split('\n')
+
-
                for (j=0;j<sensor.length;j++){
+
-
                    if (j===0){
+
-
                        sensorName = sensor[j]
+
-
                    }
+
-
                    if (originBoolean === true){
+
-
                        if (sensor[j].indexOf('//') == -1){
+
-
                            appendThis = sensor[j].replace(/[0-9]|\s|\n|\t/g,'')
+
-
                            sequence += appendThis
+
-
                        } else {
+
-
                            originBoolean = false
+
-
                        }
+
-
                    }
+
-
                    if (sensor[j].indexOf('ORIGIN') != -1){
+
-
                        originBoolean = true
+
-
                    }
+
-
                }
+
-
                sensorArray[i] = new sensorObject(sensorName,sequence)
+
-
            }
+
-
        } else if (sensors[0] == '>'){
+
-
            sensors = sensors.split('//')
+
-
            sensors.pop()
+
-
            sensorName = ''
+
-
            for (i=0;i<sensors.length;i++){
+
-
                sensor = sensors[i].split('\n')
+
-
                sequence = ''
+
-
                for (j=0;j<sensor.length;j++){
+
-
                    if (sensor[j][0] != '>'){
+
-
                        appendThis = sensor[j].replace(/[0-9]|\s|\n|\t/g,'')
+
-
                        sequence = sequence+appendThis
+
-
                    } else if (sensor[j][0] == '>'){
+
-
                        sensorName = sensor[j].replace('>','')
+
-
                    } 
+
-
                }
+
-
                sensorArray[i] = new sensorObject(sensorName,sequence)
+
-
            }
+
-
        }
+
-
        return sensorArray
+
-
}
+
-
 
+
-
function formatPartsregistryPromoters(){
+
-
        promoters = new Array()
+
-
        $("input:checkbox[name=promoter]:checked").each(function(){
+
-
            promoter = $(this).val().split(':')
+
-
            promoters.push(new sensorObject(promoter[0],promoter[2]))
+
-
        })
+
-
        return promoters
+
-
}
+
-
 
+
-
function configuratePlasmid(sensorArray,number){
+
-
memoryPlasmid.features = {}
+
-
memoryPlasmid.memoryObjects = {}
+
-
        backbone = document.plasmidForm.plasmid.value.toLowerCase()
+
-
        methyltransferases = getMethyltransferases()
+
-
        zincFingers = getZincFingers()
+
-
        linkers = getLinkers()
+
-
        mycTags = getMycTags()
+
-
        rbs = getRBS()
+
-
        terminators = getTerminators()
+
-
        plasmidSequence = formatPlasmidInput(backbone)
+
-
        memoryPlasmid.setDNA(plasmidSequence)
+
-
        for (i=0;i<sensorArray.length;i++){
+
-
    featureArray = new Array()
+
-
featureArray[0] = new feature(memoryPlasmid.dna.length+1,memoryPlasmid.dna.length+sensorArray[i].sequence.length,'Sensor',sensorArray[i].sequence,sensorArray[i].name,sensorArray[i])
+
-
            memoryPlasmid.setDNA(memoryPlasmid.dna+sensorArray[i].sequence)
+
-
            j = Math.floor((Math.random()*rbs.length))
+
-
            featureArray[1] = new feature(memoryPlasmid.dna.length+1,memoryPlasmid.dna.length+rbs[j].sequence.length,'RBS',rbs[j].sequence,rbs[j].description,rbs[j])
+
-
            memoryPlasmid.setDNA(memoryPlasmid.dna+rbs[j].sequence+randomDNA(3))
+
-
            memoryPlasmid.setDNA(memoryPlasmid.dna+'atg'+randomDNA(10))
+
-
            for (j=0;j<zincFingers.length;j++){
+
-
                if (checkOccurrence(zincFingers[j].target.toLowerCase(),memoryPlasmid.dna) === true || checkOccurrence(zincFingers[j].sequence.toLowerCase(),memoryPlasmid.dna) === true){
+
-
                    continue
+
-
                } else{
+
-
                    featureArray[2] = new feature(memoryPlasmid.dna.length+1,memoryPlasmid.dna.length+zincFingers[j].sequence.length,'Zinc Finger',zincFingers[j].sequence,'Zinc Finger '+zincFingers[j].description.split('|')[0],zincFingers[j])
+
-
                    memoryPlasmid.setDNA(memoryPlasmid.dna+zincFingers[j].sequence)
+
-
                    break
+
-
                }
+
-
            }
+
-
            j = Math.floor((Math.random()*linkers.length))
+
-
            featureArray[3] = new feature(memoryPlasmid.dna.length+1,memoryPlasmid.dna.length+linkers[j].sequence.length,'Linker',linkers[j].sequence,linkers[j].description,linkers[j])
+
-
    memoryPlasmid.setDNA(memoryPlasmid.dna+linkers[j].sequence)
+
-
            j = Math.floor((Math.random()*mycTags.length))
+
-
            featureArray[4] = new feature(memoryPlasmid.dna.length+1,memoryPlasmid.dna.length+mycTags[j].sequence.length,'Myc Tag',mycTags[j].sequence,mycTags[j].description,mycTags[j])
+
-
    memoryPlasmid.setDNA(memoryPlasmid.dna+mycTags[j].sequence)
+
-
            j = Math.floor((Math.random()*methyltransferases.length))
+
-
    featureArray[5] = new feature(memoryPlasmid.dna.length+1,memoryPlasmid.dna.length+methyltransferases[j].sequence.length,'Methyltransferase',methyltransferases[j].sequence,methyltransferases[j].description,methyltransferases[j])
+
-
            memoryPlasmid.setDNA(memoryPlasmid.dna+methyltransferases[j].sequence)
+
-
            j = Math.floor((Math.random()*terminators.length))
+
-
            featureArray[6] = new feature(memoryPlasmid.dna.length+1,memoryPlasmid.dna.length+terminators[j].sequence.length,'Terminator',terminators[j].sequence,terminators[j].description,terminators[j])
+
-
    memoryPlasmid.setDNA(memoryPlasmid.dna+terminators[j].sequence+randomDNA(10))
+
-
            memoryPlasmid.addMemoryObject(featureArray[0],featureArray[1],featureArray[2],featureArray[3],featureArray[4],featureArray[5],featureArray[6])
+
-
}
+
-
restrictionPlasmid.setDNA(memoryPlasmid.features[1].sequence)
+
-
for (item in memoryPlasmid.memoryObjects){
+
-
featureArray = new Array()
+
-
mtaseStart = restrictionPlasmid.dna.length+1
+
-
mtaseEnd = restrictionPlasmid.dna.length+memoryPlasmid.memoryObjects[item].methyltransferase.featureObject.target.length
+
-
mtaseType = 'Restriction Site'
+
-
mtaseTarget = memoryPlasmid.memoryObjects[item].methyltransferase.featureObject.target.toLowerCase()
+
-
mtaseDescription = memoryPlasmid.memoryObjects[item].methyltransferase.featureObject.description+' restriction site'
+
-
featureArray[0] = new feature(mtaseStart,mtaseEnd,mtaseType,mtaseTarget,mtaseDescription)
+
-
restrictionPlasmid.setDNA(restrictionPlasmid.dna+mtaseTarget)
+
-
zfStart = restrictionPlasmid.dna.length+1
+
-
zfEnd = restrictionPlasmid.dna.length+memoryPlasmid.memoryObjects[item].zincFinger.featureObject.target.length
+
-
zfType = 'Restriction Site'
+
-
zfTarget = memoryPlasmid.memoryObjects[item].zincFinger.featureObject.target
+
-
zfDescription = memoryPlasmid.memoryObjects[item].zincFinger.featureObject.description+' restriction site'
+
-
featureArray[1] = new feature(zfStart,zfEnd,zfType,zfTarget,zfDescription)
+
-
restrictionPlasmid.setDNA(restrictionPlasmid.dna+mtaseTarget)
+
-
restrictionPlasmid.mtaseTarget = featureArray[0]
+
-
restrictionPlasmid.zfTarget = featureArray[1]
+
-
}
+
-
json = createJSONMemory(number)
+
-
//genbankMemory()
+
-
$('#visualizationButtons').append('<input type="hidden" name="json'+number+'" value="'+escape(JSON.stringify(json))+'"/><input class="submit" type="submit" value="Memory Plasmid '+(number+1)+'" onclick="visualization('+number+');return false"/>');
+
-
}
+
-
 
+
-
function setup(){
+
-
$('#visualizationButtons').empty()
+
-
$('#infovis').empty()
+
-
$('#readout').empty()
+
-
addForbiddenSequences()
+
-
sensors = document.plasmidForm.sensors.value.toLowerCase()
+
-
sensorArray = formatSensors(sensors)
+
-
        promoters = formatPartsregistryPromoters()
+
-
        sensorArray = promoters.concat(sensorArray)
+
-
tempArray = new Array()
+
-
j = 0
+
-
number = 0
+
-
targetSites = new Array()
+
-
for (sensor in sensorArray){
+
-
tempArray[j] = sensorArray[sensor]
+
-
j++
+
-
if (j%5 === 0 && j !== 0){
+
-
configuratePlasmid(tempArray,number)
+
-
number++
+
-
tempArray = new Array()
+
-
j = 0
+
-
for (item in memoryPlasmid.memoryObjects){
+
-
site = new Object()
+
-
site.zincFingerDescription = memoryPlasmid.memoryObjects[item].zincFinger.featureObject.description
+
-
site.zincFinger = memoryPlasmid.memoryObjects[item].zincFinger.featureObject.target
+
-
site.zincFingerLength = site.zincFinger.length
+
-
site.methyltransferaseDescription = memoryPlasmid.memoryObjects[item].methyltransferase.featureObject.description
+
-
site.methyltransferase = memoryPlasmid.memoryObjects[item].methyltransferase.featureObject.target
+
-
site.methyltransferaseLength = site.methyltransferase.length
+
-
site.sensor = memoryPlasmid.memoryObjects[item].sensor.description
+
-
targetSites.push(site)
+
-
}
+
-
}
+
-
}
+
-
if (j%5 !== 0){
+
-
configuratePlasmid(tempArray,number)
+
-
for (item in memoryPlasmid.memoryObjects){
+
-
site = new Object()
+
-
site.zincFingerDescription = memoryPlasmid.memoryObjects[item].zincFinger.featureObject.description
+
-
site.zincFinger = memoryPlasmid.memoryObjects[item].zincFinger.featureObject.target
+
-
site.zincFingerLength = site.zincFinger.length
+
-
site.methyltransferaseDescription = memoryPlasmid.memoryObjects[item].methyltransferase.featureObject.description
+
-
site.methyltransferase = memoryPlasmid.memoryObjects[item].methyltransferase.featureObject.target
+
-
site.methyltransferaseLength = site.methyltransferase.length
+
-
site.sensor = memoryPlasmid.memoryObjects[item].sensor.description
+
-
targetSites.push(site)
+
-
}
+
-
}
+
-
//genbankRestriction(targetSites)
+
-
json = createJSONRestriction(targetSites)
+
-
$('#visualizationButtons').append('<input type="hidden" name="json-1" value="'+escape(JSON.stringify(json))+'"/><input class="submit" type="submit" value="Restriction Plasmid" onclick="visualization(-1);return false"/>');
+
-
$('#readout').append('<input type="textfield" name="readout" value=""/><input class="submit" type="submit" value="Submit" onClick="getReadout();return false"/>');
+
-
}
+
-
 
+
-
function getReadout(){
+
-
inputArray = new Array()
+
-
json = JSON.parse(unescape($(':input[name=json-1]').val()))
+
-
inputs = $(':input[name=readout]').val()
+
-
inputArray = inputs.split(',')
+
-
totalLength = json.children[0].data.length
+
-
uncutArray = new Array()
+
-
i = 0
+
-
for (child in json.children){
+
-
totalLength+=json.children[child].data.length
+
-
if (json.children[child].data.description.indexOf('Methyltransferase') != -1){
+
-
uncutArray[i] = [json.children[child].id,totalLength]
+
-
i++
+
-
}
+
-
}
+
-
bandsArray = new Array ()
+
-
j = 0
+
-
for (item in uncutArray){
+
-
i = 0
+
-
tempBandArray = new Array()
+
-
tempBandArray[i] = [uncutArray[item][1],uncutArray[item][0]]
+
-
i++
+
-
for (bandArray in bandsArray){
+
-
for (band in bandsArray[bandArray]){
+
-
tempBandArray[i] = [uncutArray[item][1] - bandsArray[bandArray][band][0],uncutArray[item][0]]
+
-
i++
+
-
}
+
-
}
+
-
bandsArray[j] = tempBandArray
+
-
j++
+
-
}
+
-
matchingBands = new Array()
+
-
i = 0
+
-
for (input in inputArray){
+
-
difference = 100000000000
+
-
bandSize = inputArray[input]
+
-
for (bandArray in bandsArray){
+
-
for (band in bandsArray[bandArray]){
+
-
if (bandSize > bandsArray[bandArray][band][0]){
+
-
tempDifference = bandSize - bandsArray[bandArray][band][0]
+
-
} else{
+
-
tempDifference = bandsArray[bandArray][band][0] - bandSize
+
-
}
+
-
if (tempDifference < difference){
+
-
matchingBand = bandsArray[bandArray][band][1]
+
-
difference = tempDifference
+
-
}
+
-
}
+
-
}
+
-
matchingBands[i] = matchingBand
+
-
i++
+
-
}
+
-
i = 0
+
-
sensedSignals = new Array()
+
-
for (matchingBand in matchingBands){
+
-
for (child in json.children){
+
-
if (json.children[child].id == matchingBands[matchingBand]){
+
-
sensedSignals[i] = json.children[child].data.sensor
+
-
i++
+
-
}
+
-
}
+
-
}
+
-
for (signal in sensedSignals){
+
-
$('#readout').append('<br>'+sensedSignals[signal])
+
-
}
+
-
}
+
-
 
+
-
function createJSONRestriction(targetSites){
+
-
json = {
+
-
      "children": [],
+
-
      "data": {
+
-
        "$type": "none",
+
-
      },
+
-
      "id": "Source",
+
-
      "name": "Restriction Plasmid"
+
-
    };
+
-
+
-
json.children[0] = {}
+
-
json.children[0].data = {}
+
-
json.children[0].data.description = memoryPlasmid.features[1].description
+
-
json.children[0].data.$color = '#B2ABF4'
+
-
json.children[0].data.length = memoryPlasmid.features[1].end - memoryPlasmid.features[1].start
+
-
json.children[0].data.$angularWidth = 1000
+
-
json.children[0].data.type = memoryPlasmid.features[1].type
+
-
json.children[0].data.dna = memoryPlasmid.dna
+
-
json.children[0].children = []
+
-
json.children[0].name = memoryPlasmid.features[1].description
+
-
json.children[0].id = memoryPlasmid.features[1].description
+
-
totalLength = memoryPlasmid.dna.length
+
-
i = 1
+
-
for (item in targetSites){
+
-
site = targetSites[item]
+
-
json.children[i] = {}
+
-
json.children[i].data = {}
+
-
json.children[i].children = []
+
-
json.children[i].data.description = '120bp random DNA'
+
-
json.children[i].data.$color = '#FFFF00'
+
-
json.children[i].data.length = 120
+
-
json.children[i].data.$angularWidth = 1000
+
-
json.children[i].data.dna = randomDNA(120+i*10)
+
-
json.children[i].name = '120bp DNA'
+
-
json.children[i].id = i
+
-
i++
+
-
json.children[i] = {}
+
-
json.children[i].data = {}
+
-
json.children[i].children = []
+
-
json.children[i].data.description = site.zincFingerDescription
+
-
json.children[i].data.$color = '#FF0000'
+
-
json.children[i].data.length = site.zincFingerLength
+
-
json.children[i].data.$angularWidth = 1000
+
-
json.children[i].data.dna = site.zincFinger
+
-
json.children[i].name = site.zincFingerDescription.split('|')[0]+'|'+site.zincFingerDescription.split('|')[1]
+
-
json.children[i].id = i
+
-
i++
+
-
json.children[i] = {}
+
-
json.children[i].data = {}
+
-
json.children[i].children = []
+
-
json.children[i].data.description = '120bp random DNA'
+
-
json.children[i].data.$color = '#FFFF00'
+
-
json.children[i].data.length = 120
+
-
json.children[i].data.$angularWidth = 1000
+
-
json.children[i].data.dna = randomDNA(120)
+
-
json.children[i].name = '120bp DNA'
+
-
json.children[i].id = i
+
-
i++
+
-
json.children[i] = {}
+
-
json.children[i].data = {}
+
-
json.children[i].children = []
+
-
json.children[i].data.description = 'Methyltransferase: '+site.methyltransferaseDescription
+
-
json.children[i].data.$color = '#0000CD'
+
-
json.children[i].data.length = site.methyltransferaseLength
+
-
json.children[i].data.$angularWidth = 1000
+
-
json.children[i].data.dna = site.methyltransferase
+
-
json.children[i].data.sensor = site.sensor
+
-
json.children[i].name = site.methyltransferaseDescription.split('|')[0]
+
-
json.children[i].id = i
+
-
i++
+
-
json.children[i] = {}
+
-
json.children[i].data = {}
+
-
json.children[i].children = []
+
-
json.children[i].data.description = '120bp random DNA'
+
-
json.children[i].data.$color = '#FFFF00'
+
-
json.children[i].data.length = 120
+
-
json.children[i].data.$angularWidth = 1000
+
-
json.children[i].data.dna = randomDNA(120)
+
-
json.children[i].name = '120bp DNA'
+
-
json.children[i].id = i
+
-
i++
+
-
json.children[i] = {}
+
-
json.children[i].data = {}
+
-
json.children[i].children = []
+
-
json.children[i].data.description = site.zincFingerDescription
+
-
json.children[i].data.$color = '#FF0000'
+
-
json.children[i].data.length = site.zincFingerLength
+
-
json.children[i].data.$angularWidth = 1000
+
-
json.children[i].data.dna = site.zincFinger
+
-
json.children[i].name = site.zincFingerDescription.split('|')[0]+'|'+site.zincFingerDescription.split('|')[1]
+
-
json.children[i].id = i
+
-
i++
+
-
}
+
-
return json
+
-
}
+
-
 
+
-
function createJSONMemory(number){
+
-
var json = {}
+
-
json = {
+
-
      "children": [],
+
-
      "data": {
+
-
        "$type": "none",
+
-
      },
+
-
      "id": "Source",
+
-
      "name": "Memory Plasmid"
+
-
    };
+
-
+
-
json.children[0] = {}
+
-
json.children[0].data = {}
+
-
json.children[0].data.description = memoryPlasmid.features[1].description
+
-
json.children[0].data.$color = '#B2ABF4'
+
-
json.children[0].data.length = memoryPlasmid.features[1].end - memoryPlasmid.features[1].start
+
-
json.children[0].data.$angularWidth = 1000
+
-
json.children[0].data.type = memoryPlasmid.features[1].type
+
-
json.children[0].data.dna = memoryPlasmid.dna
+
-
json.children[0].children = []
+
-
json.children[0].name = memoryPlasmid.features[1].description
+
-
json.children[0].id = memoryPlasmid.features[1].description
+
-
    i = 1
+
-
    for (memoryObject in memoryPlasmid.memoryObjects){
+
-
for (item in memoryPlasmid.memoryObjects[memoryObject]){
+
-
json.children[i] = {}
+
-
json.children[i].children = []
+
-
json.children[i].data = {}
+
-
json.children[i].data.description = memoryPlasmid.memoryObjects[memoryObject][item].description
+
-
type = memoryPlasmid.memoryObjects[memoryObject][item].type
+
-
if (type == 'Sensor'){
+
-
color = '#00FFFF'
+
-
} else if (type == 'RBS'){
+
-
color = '#FFFF00'
+
-
} else if (type == 'Zinc Finger'){
+
-
color = '#800080'
+
-
} else if (type == 'Linker'){
+
-
color = '#00FF00'
+
-
} else if (type == 'Myc Tag'){
+
-
color = '#FF00FF'
+
-
} else if (type == 'Methyltransferase'){
+
-
color = '#FFA500'
+
-
} else if (type == 'Terminator'){
+
-
color = '#FF0000'
+
-
} else{
+
-
color = '#B2ABF4'
+
-
}
+
-
json.children[i].data.$color = color
+
-
json.children[i].data.length = memoryPlasmid.memoryObjects[memoryObject][item].end - memoryPlasmid.memoryObjects[memoryObject][item].start
+
-
json.children[i].data.$angularWidth = 1000
+
-
json.children[i].data.type = type
+
-
json.children[i].data.dna = memoryPlasmid.memoryObjects[memoryObject][item].sequence
+
-
json.children[i].id = i
+
-
if (memoryPlasmid.memoryObjects[memoryObject][item].description.length > 14){
+
-
json.children[i].name = memoryPlasmid.memoryObjects[memoryObject][item].description.substring(0,14)
+
-
} else{
+
-
json.children[i].name = memoryPlasmid.memoryObjects[memoryObject][item].description
+
-
}
+
-
i++
+
-
}
+
-
}
+
-
return json
+
-
 
+
-
    //end
+
-
}
+
-
 
+
-
</script>
+
-
</head>
+
-
<body>
+
-
<p>
+
-
<form name='plasmidForm' class='rounded'>
+
-
<div class='field'>
+
-
    <label for='Plasmid'>Plasmid:</label>
+
-
    <textarea type='text' class='input' name='plasmid' id='plasmid'>
+
-
</textarea>
+
-
    <p class="hint">Enter your plasmid in fasta or genbank format</p>
+
-
</div>
+
-
<br>
+
-
<div class='field'>
+
-
    <label for='sensors'>promoters:</label>
+
-
    <textarea type='text' class='input' name='sensors' id='sensors'></textarea>
+
-
    <p class="hint">Enter your sensors in fasta or genbank format</p>
+
-
</div>
+
-
<input type='hidden' name='zf' value='>N1|1|http://web.iitd.ac.in/~sundar/zifbase/prot_disp1.php?id=N1PE3130|Engineered construct|C2H2 (3F)|GGGGTAGAA
+
-
gcgcaggcggcgctggaaccgaaagaaaaaccgtatgcgtgcccggaatgcggcaaaagc
+
-
tttagccagagcagcaacctggtgcgccatcagcgcacccataccggcgaaaaaccgtat
+
-
aaatgcccggaatgcggcaaaagctttagccagagcagcagcctggtgcgccatcagcgc
+
-
acccataccggcgaaaaaccgtataaatgcccggaatgcggcaaaagctttagccgcagc
+
-
gataaactggtgcgccatcagcgcacccataccggcaaaaaaaccagcggccaggcgggc
+
-
>B3|2|http://web.iitd.ac.in/~sundar/zifbase/prot_disp1.php?id=B3PE3129|Engineered construct|C2H2 (3F)|GGAGGGGAC
+
-
gcgcaggcggcgctggaaccgaaagaaaaaccgtatgcgtgcccggaatgcggcaaaagc
+
-
tttagcgatccgggcaacctggtgcgccatcagcgcacccataccggcgaaaaaccgtat
+
-
aaatgcccggaatgcggcaaaagctttagccgcagcgataaactggtgcgccatcagcgc
+
-
acccataccggcgaaaaaccgtataaatgcccggaatgcggcaaaagctttagccagagc
+
-
agccatctggtgcgccatcagcgcacccataccggcaaaaaaaccagcggccaggcgggc
+
-
>Anti-BcrAbl|3|http://web.iitd.ac.in/~sundar/zifbase/prot_disp1.php?id=ABAE4134|Engineered construct|C2H2 (4F)|GACGCAGAAGCC
+
-
gcggaagaaaaaccgtttcagtgccgcatttgcatgcgcaactttagcgatcgcagcagc
+
-
ctgacccgccatacccgcacccataccggcgaaaaaccgtttcagtgccgcatttgcatg
+
-
cgcaactttagccagggcggcaacctggtgcgccatctgcgcacccataccggcgaaaaa
+
-
ccgtttcagtgccgcatttgcatgcgcaactttagccaggcggcgaccctgcagcgccat
+
-
ctgaaaacccataccggcgaaaaaccgtttcagtgccgcatttgcatgcgcaactttagc
+
-
gatcgcagcaacctggaacgccatacccgcacccataccggcgaaaaactggaacgcccg
+
-
catcgcgat
+
-
>C7-C7|4|http://web.iitd.ac.in/~sundar/zifbase/prot_disp1.php?id=C72E6127|Engineered construct|C2H2 (2x3F)|GCGTGGGCGGCGTGGGCG
+
-
gaacgcccgtatgcgtgcccggtggaaagctgcgatcgccgctttagcaaaagcgcggat
+
-
ctgaaacgccatattcgcattcataccggccagaaaccgtttcagtgccgcatttgcatg
+
-
cgcaactttagccgcagcgatcatctgaccacccatattcgcacccataccggcgaaaaa
+
-
ccgtttgcgtgcgatatttgcggccgcaaatttgcgcgcagcgatgaacgcaaacgccat
+
-
accaaaattcataccggcgaaaaaccgtatgcgtgcccggtggaaagctgcgatcgccgc
+
-
tttagcaaaagcgcggatctgaaacgccatattcgcattcataccggccagaaaccgttt
+
-
cagtgccgcatttgcatgcgcaactttagccgcagcgatcatctgaccacccatattcgc
+
-
acccataccggcgaaaaaccgtttgcgtgcgatatttgcggccgcaaatttgcgcgcagc
+
-
gatgaacgcaaacgccataccaaaattcatctgcgccagaaagat
+
-
>3x2F ZMS|5|http://web.iitd.ac.in/~sundar/zifbase/prot_disp1.php?id=ZMSE6114|Engineered construct|C2H2 (3x2F)|GCGGACGCGGCGTGGGCG
+
-
gaacgcccgtatgcgtgcccggtggaaagctgcgatcgccgctttagccgcagcgatgaa
+
-
ctgacccgccatattcgcattcataccggccagaaaccgtttcagtgccgcatttgcatg
+
-
cgcaactttagccgcagcgatcatctgaccacccatattcgcacccataccggcggcgaa
+
-
aaaccgtttgcgtgcgatatttgcggccgcaaatttgcgcgcagcgatgaacgcaaacgc
+
-
cataccaaaattcataccggcgaacgcccgtatgcgtgcccggtggaaagctgcgatcgc
+
-
cgctttagccgcagcgatgaactgacccgccatattcgcattcataccggcggccagaaa
+
-
ccgtttcagtgccgcatttgcatgcgcaactttagcgatcgcagcaacctggaacgccat
+
-
acccgcacccataccggcgaaaaaccgtttgcgtgcgatatttgcggccgcaaatttgcg
+
-
cgcagcgatgaacgcaaacgccataccaaaattcatctgcgccagaaagat
+
-
>268/NRE|6|http://web.iitd.ac.in/~sundar/zifbase/prot_disp1.php?id=NRCE6113|Engineered construct|C2H2 (2x3F)|AAGGGTTCAGGCGTGGGCG
+
-
gaacgcccgtatgcgtgcccggtggaaagctgcgatcgccgctttagccgcagcgatgaa
+
-
ctgacccgccatattcgcattcataccggccagaaaccgtttcagtgccgcatttgcatg
+
-
cgcaactttagccgcagcgatcatctgaccacccatattcgcacccataccggcgaaaaa
+
-
ccgtttgcgtgcgatatttgcggccgcaaatttgcgcgcagcgatgaacgcaaacgccat
+
-
accaaaattcatctgcgccagaaagatggcgaacgcccgtatgcgtgcccggtggaaagc
+
-
tgcgatcgccgctttagccagagccatgatctgaccaaacatattcgcattcataccggc
+
-
cagaaaccgtttcagtgccgcatttgcatgcgcaactttagcgatagcagcaaactgagc
+
-
cgccatattcgcacccataccggcgaaaaaccgtttgcgtgcgatatttgcggccgcaaa
+
-
tttgcgcgcccggataaccgcaccgcgcataccaaaattcatctgcgccagaaagat
+
-
>Sp1C-C7|7|http://web.iitd.ac.in/~sundar/zifbase/prot_disp1.php?id=SC7E6128|Engineered construct|C2H2 (2x3F)|GCGTGGGCGGGGGCGGGG
+
-
gatccgggcaaaaaaaaacagcatatttgccatattcagggctgcggcaaagtgtatggc
+
-
aaaaccagccatctgcgcgcgcatctgcgctggcataccggcgaacgcccgtttatgtgc
+
-
acctggagctattgcggcaaacgctttacccgcagcgatgaactgcagcgccataaacgc
+
-
acccataccggcgaaaaaaaatttgcgtgcccggaatgcccgaaacgctttatgcgcagc
+
-
gatcatctgagcaaacatattaaaacccataccggcgaaaaaccgtatgcgtgcccggtg
+
-
gaaagctgcgatcgccgctttagcaaaagcgcggatctgaaacgccatattcgcattcat
+
-
accggccagaaaccgtttcagtgccgcatttgcatgcgcaactttagccgcagcgatcat
+
-
ctgaccacccatattcgcacccataccggcgaaaaaccgtttgcgtgcgatatttgcggc
+
-
cgcaaatttgcgcgcagcgatgaacgcaaacgccataccaaaattcatctgcgccagaaa
+
-
gat
+
-
>268//NRE|8|http://web.iitd.ac.in/~sundar/zifbase/prot_disp1.php?id=NRBE6112|Engineered construct|C2H2 (2x3F)|AAGGGTTCAGTGCGTGGGCG
+
-
gaacgcccgtatgcgtgcccggtggaaagctgcgatcgccgctttagccgcagcgatgaa
+
-
ctgacccgccatattcgcattcataccggccagaaaccgtttcagtgccgcatttgcatg
+
-
cgcaactttagccgcagcgatcatctgaccacccatattcgcacccataccggcgaaaaa
+
-
ccgtttgcgtgcgatatttgcggccgcaaatttgcgcgcagcgatgaacgcaaacgccat
+
-
accaaaattcatctgcgccagaaagatggcggcggcagcgaacgcccgtatgcgtgcccg
+
-
gtggaaagctgcgatcgccgctttagccagagccatgatctgaccaaacatattcgcatt
+
-
cataccggccagaaaccgtttcagtgccgcatttgcatgcgcaactttagcgatagcagc
+
-
aaactgagccgccatattcgcacccataccggcgaaaaaccgtttgcgtgcgatatttgc
+
-
ggccgcaaatttgcgcgcccggataaccgcaccgcgcataccaaaattcatctgcgccag
+
-
aaagat
+
-
>E2C|9|http://web.iitd.ac.in/~sundar/zifbase/prot_disp1.php?id=E2CE6125|Engineered construct|C2H2 (2x3F)|GGGGCCGGAGCCGCAGTG
+
-
gcgcaggcggcgctggaaccgggcgaaaaaccgtatgcgtgcccggaatgcggcaaaagc
+
-
tttagccgcaaagatagcctggtgcgccatcagcgcacccataccggcgaaaaaccgtat
+
-
aaatgcccggaatgcggcaaaagctttagccagagcggcgatctgcgccgccatcagcgc
+
-
acccataccggcgaaaaaccgtataaatgcccggaatgcggcaaaagctttagcgattgc
+
-
cgcgatctggcgcgccatcagcgcacccataccggcgaaaaaccgtatgcgtgcccggaa
+
-
tgcggcaaaagctttagccagagcagccatctggtgcgccatcagcgcacccataccggc
+
-
gaaaaaccgtataaatgcccggaatgcggcaaaagctttagcgattgccgcgatctggcg
+
-
cgccatcagcgcacccataccggcgaaaaaccgtataaatgcccggaatgcggcaaaagc
+
-
tttagccgcagcgataaactggtgcgccatcagcgcacccataccggcaaaaaaaccagc
+
-
ggccaggcgggc
+
-
>ZFPAP3|10|http://web.iitd.ac.in/~sundar/zifbase/prot_disp1.php?id=AP3E6135|Engineered construct|C2H2 (2x3F)|TACTTCTTCAACTCCATC
+
-
gcgcaggcggcgctggaaccgaaagaaaaaccgtatgcgtgcccggaatgcggcaaaagc
+
-
tttagccagagcagcagcctggtgcgccatcagcgcacccataccggcgaaaaaccgtat
+
-
aaatgcccggaatgcggcaaaagctttagccagagcagcaacctggtgcgccatcagcgc
+
-
acccataccggcgaaaaaccgtataaatgcccggaatgcggcaaaagctttagccagagc
+
-
agcaacctggtgcgccatcagcgcacccataccggcgaaaaaccgtatgcgtgcccggaa
+
-
tgcggcaaaagctttagcaccagcggcagcctggtgcgccatcagcgcacccataccggc
+
-
gaaaaaccgtataaatgcccggaatgcggcaaaagctttagccagagcagccatctggtg
+
-
cgccatcagcgcacccataccggcgaaaaaccgtataaatgcccggaatgcggcaaaagc
+
-
tttagcaccagcggcaacctggtgcgccatcagcgcacccataccggcaaaaaaaccagc
+
-
ggccaggcgggc
+
-
>E3|11|http://web.iitd.ac.in/~sundar/zifbase/prot_disp1.php?id=E3PE6126|Engineered construct|C2H2 (2x3F)|GGAGCCGGAGCCGGAGTC
+
-
gcgcaggcggcgctggaaccgggcgaaaaaccgtatgcgtgcccggaatgcggcaaaagc
+
-
tttagcgatccgggcgcgctggtgcgccatcagcgcacccataccggcgaaaaaccgtat
+
-
aaatgcccggaatgcggcaaaagctttagccagagcagccatctggtgcgccatcagcgc
+
-
acccataccggcgaaaaaccgtataaatgcccggaatgcggcaaaagctttagcgattgc
+
-
cgcgatctggcgcgccatcagcgcacccataccggcgaaaaaccgtatgcgtgcccggaa
+
-
tgcggcaaaagctttagccagagcagccatctggtgcgccatcagcgcacccataccggc
+
-
gaaaaaccgtataaatgcccggaatgcggcaaaagctttagcgattgccgcgatctggcg
+
-
cgccatcagcgcacccataccggcgaaaaaccgtataaatgcccggaatgcggcaaaagc
+
-
tttagccagagcagccatctggtgcgccatcagcgcacccataccggcaaaaaaaccagc
+
-
ggccaggcgggc
+
-
>MUT|13|http://web.iitd.ac.in/~sundar/zifbase/prot_disp1.php?id=MUTE3115|Engineered construct|C2H2 (3F)|GCGGACGCG
+
-
gaacgcccgtatgcgtgcccggtggaaagctgcgatcgccgctttagccgcagcgatgaa
+
-
ctgacccgccatattcgcattcataccggccagaaaccgtttcagtgccgcatttgcatg
+
-
cgcaactttagcgatcgcagcaacctggaacgccatacccgcacccataccggcgaaaaa
+
-
ccgtttgcgtgcgatatttgcggccgcaaatttgcgcgcagcgatgaacgcaaacgccat
+
-
accaaaattcatctgcgccagaaagat
+
-
>NRE|14|http://web.iitd.ac.in/~sundar/zifbase/prot_disp1.php?id=NRAE3111|Engineered construct|C2H2 (3F)|AAGGGTTCA
+
-
gaacgcccgtatgcgtgcccggtggaaagctgcgatcgccgctttagccagagccatgat
+
-
ctgaccaaacatattcgcattcataccggccagaaaccgtttcagtgccgcatttgcatg
+
-
cgcaactttagcgatagcagcaaactgagccgccatattcgcacccataccggcgaaaaa
+
-
ccgtttgcgtgcgatatttgcggccgcaaatttgcgcgcccggataaccgcaccgcgcat
+
-
accaaaattcatctgcgccagaaagat
+
-
>GNG-GA1|15|http://web.iitd.ac.in/~sundar/zifbase/prot_disp1.php?id=GA1E3168|Engineered construct|C2H2 (3F)|GAGGAGGGG
+
-
gatccgggcaaaaaaaaacagcatatttgccatattcagggctgcggcaaagtgtatggc
+
-
cgcagcgatcatctggcgcgccatctgcgctggcataccggcgaacgcccgtttatgtgc
+
-
acctggagctattgcggcaaacgctttacccgcagcgataacctggcgcgccataaacgc
+
-
acccataccggcgaaaaaaaatttgcgtgcccggaatgcccgaaacgctttatgcgcagc
+
-
gataacctgacccgccatattaaaacccatcagaacaaaaaa
+
-
>GNG-GA2|16|http://web.iitd.ac.in/~sundar/zifbase/prot_disp1.php?id=GA2E3169|Engineered construct|C2H2 (3F)|GTGGAGGGG
+
-
gatccgggcaaaaaaaaacagcatatttgccatattcagggctgcggcaaagtgtatggc
+
-
cgcagcgatcatctggcgcgccatctgcgctggcataccggcgaacgcccgtttatgtgc
+
-
acctggagctattgcggcaaacgctttacccgcagcgataacctggcgcgccataaacgc
+
-
acccataccggcgaaaaaaaatttgcgtgcccggaatgcccgaaacgctttatgcgcagc
+
-
gatgcgctgacccgccatattaaaacccatcagaacaaaaaa
+
-
>GNG-GA3|17|http://web.iitd.ac.in/~sundar/zifbase/prot_disp1.php?id=GA3E3170|Engineered construct|C2H2 (3F)|GGGGAGGGG
+
-
gatccgggcaaaaaaaaacagcatatttgccatattcagggctgcggcaaagtgtatggc
+
-
cgcagcgatcatctggcgcgccatctgcgctggcataccggcgaacgcccgtttatgtgc
+
-
acctggagctattgcggcaaacgctttacccgcagcgataacctggcgcgccataaacgc
+
-
acccataccggcgaaaaaaaatttgcgtgcccggaatgcccgaaacgctttatgcgcagc
+
-
gatcatctgagccgccatattaaaacccatcagaacaaaaaa
+
-
>GNG-GT3|18|http://web.iitd.ac.in/~sundar/zifbase/prot_disp1.php?id=GT3E3174|Engineered construct|C2H2 (3F)|GGGGTGGGG
+
-
gatccgggcaaaaaaaaacagcatatttgccatattcagggctgcggcaaagtgtatggc
+
-
cgcagcgatcatctggcgcgccatctgcgctggcataccggcgaacgcccgtttatgtgc
+
-
acctggagctattgcggcaaacgctttacccgcagcgatgcgctgagccgccataaacgc
+
-
acccataccggcgaaaaaaaatttgcgtgcccggaatgcccgaaacgctttatgcgcagc
+
-
gatcatctgagccgccatattaaaacccatcagaacaaaaaa
+
-
>GNG-GT2|19|http://web.iitd.ac.in/~sundar/zifbase/prot_disp1.php?id=GT2E3173|Engineered construct|C2H2 (3F)|GTGGTGGGG
+
-
gatccgggcaaaaaaaaacagcatatttgccatattcagggctgcggcaaagtgtatggc
+
-
cgcagcgatcatctggcgcgccatctgcgctggcataccggcgaacgcccgtttatgtgc
+
-
acctggagctattgcggcaaacgctttacccgcagcgatgcgctgagccgccataaacgc
+
-
acccataccggcgaaaaaaaatttgcgtgcccggaatgcccgaaacgctttatgcgcagc
+
-
gatgcgctgacccgccatattaaaacccatcagaacaaaaaa
+
-
>GNG-GT1|20|http://web.iitd.ac.in/~sundar/zifbase/prot_disp1.php?id=GT1E3172|Engineered construct|C2H2 (3F)|GAGGTGGGG
+
-
gatccgggcaaaaaaaaacagcatatttgccatattcagggctgcggcaaagtgtatggc
+
-
cgcagcgatcatctggcgcgccatctgcgctggcataccggcgaacgcccgtttatgtgc
+
-
acctggagctattgcggcaaacgctttacccgcagcgatgcgctgagccgccataaacgc
+
-
acccataccggcgaaaaaaaatttgcgtgcccggaatgcccgaaacgctttatgcgcagc
+
-
gataacctgacccgccatattaaaacccatcagaacaaaaaa
+
-
>GNG-GG4|21|http://web.iitd.ac.in/~sundar/zifbase/prot_disp1.php?id=GG4E4179|Engineered construct|C2H2 (3F)|GCGGGGGGG
+
-
gatccgggcaaaaaaaaacagcatatttgccatattcagggctgcggcaaagtgtatggc
+
-
cgcagcgatcatctggcgcgccatctgcgctggcataccggcgaacgcccgtttatgtgc
+
-
acctggagctattgcggcaaacgctttacccgcagcgatcatctgacccgccataaacgc
+
-
acccataccggcgaaaaaaaatttgcgtgcccggaatgcccgaaacgctttatgcgcagc
+
-
gatgatctgacccgccatattaaaacccatcagaacaaaaaa
+
-
>GNG-GA4|22|http://web.iitd.ac.in/~sundar/zifbase/prot_disp1.php?id=GA4E3171|Engineered construct|C2H2 (3F)|GCGGAGGGG
+
-
gatccgggcaaaaaaaaacagcatatttgccatattcagggctgcggcaaagtgtatggc
+
-
cgcagcgatcatctggcgcgccatctgcgctggcataccggcgaacgcccgtttatgtgc
+
-
acctggagctattgcggcaaacgctttacccgcagcgataacctggcgcgccataaacgc
+
-
acccataccggcgaaaaaaaatttgcgtgcccggaatgcccgaaacgctttatgcgcagc
+
-
gatgatctgacccgccatattaaaacccatcagaacaaaaaa
+
-
>GNG-GC1|23|http://web.iitd.ac.in/~sundar/zifbase/prot_disp1.php?id=GC1E3180|Engineered construct|C2H2 (3F)|GAGGCGGGG
+
-
gatccgggcaaaaaaaaacagcatatttgccatattcagggctgcggcaaagtgtatggc
+
-
cgcagcgatcatctggcgcgccatctgcgctggcataccggcgaacgcccgtttatgtgc
+
-
acctggagctattgcggcaaacgctttacccgcagcgatgatctgcagcgccataaacgc
+
-
acccataccggcgaaaaaaaatttgcgtgcccggaatgcccgaaacgctttatgcgcagc
+
-
gataacctgacccgccatattaaaacccatcagaacaaaaaa
+
-
>GNG-GG3|24|http://web.iitd.ac.in/~sundar/zifbase/prot_disp1.php?id=GG3E3178|Engineered construct|C2H2 (3F)|GGGGGGGGG
+
-
gatccgggcaaaaaaaaacagcatatttgccatattcagggctgcggcaaagtgtatggc
+
-
cgcagcgatcatctggcgcgccatctgcgctggcataccggcgaacgcccgtttatgtgc
+
-
acctggagctattgcggcaaacgctttacccgcagcgatcatctgacccgccataaacgc
+
-
acccataccggcgaaaaaaaatttgcgtgcccggaatgcccgaaacgctttatgcgcagc
+
-
gatcatctgagccgccatattaaaacccatcagaacaaaaaa
+
-
>GNG-GG2|25|http://web.iitd.ac.in/~sundar/zifbase/prot_disp1.php?id=GG2E3177|Engineered construct|C2H2 (3F)|GTGGGGGGG
+
-
gatccgggcaaaaaaaaacagcatatttgccatattcagggctgcggcaaagtgtatggc
+
-
cgcagcgatcatctggcgcgccatctgcgctggcataccggcgaacgcccgtttatgtgc
+
-
acctggagctattgcggcaaacgctttacccgcagcgatcatctgacccgccataaacgc
+
-
acccataccggcgaaaaaaaatttgcgtgcccggaatgcccgaaacgctttatgcgcagc
+
-
gatgcgctgacccgccatattaaaacccatcagaacaaaaaa
+
-
>GNG-GC2|26|http://web.iitd.ac.in/~sundar/zifbase/prot_disp1.php?id=GC2E3181|Engineered construct|C2H2 (3F)|GTGGCGGGG
+
-
gatccgggcaaaaaaaaacagcatatttgccatattcagggctgcggcaaagtgtatggc
+
-
cgcagcgatcatctggcgcgccatctgcgctggcataccggcgaacgcccgtttatgtgc
+
-
acctggagctattgcggcaaacgctttacccgcagcgatgatctgcagcgccataaacgc
+
-
acccataccggcgaaaaaaaatttgcgtgcccggaatgcccgaaacgctttatgcgcagc
+
-
gatgcgctgacccgccatattaaaacccatcagaacaaaaaa
+
-
>GNG-GC3|27|http://web.iitd.ac.in/~sundar/zifbase/prot_disp1.php?id=GC3E3182|Engineered construct|C2H2 (3F)|GGGGCGGGG
+
-
gatccgggcaaaaaaaaacagcatatttgccatattcagggctgcggcaaagtgtatggc
+
-
cgcagcgatcatctggcgcgccatctgcgctggcataccggcgaacgcccgtttatgtgc
+
-
acctggagctattgcggcaaacgctttacccgcagcgatgatctgcagcgccataaacgc
+
-
acccataccggcgaaaaaaaatttgcgtgcccggaatgcccgaaacgctttatgcgcagc
+
-
gatcatctgagccgccatattaaaacccatcagaacaaaaaa'
+
-
>
+
-
<div class="form-checkbox">
+
-
<input type="checkbox" value="BBa_K086017:unmodified Lutz-Bujard LacO promoter:ttgtgagcggataacaagatactgagcaca" id="BBa_K086017" name="promoter" title="unmodified Lutz-Bujard LacO promoter"/>
+
-
<label for="BBa_K086017">BBa_K086017</label>
+
-
<input type="checkbox" value="BBa_K086018:modified Lutz-Bujard LacO promoter,with alternative sigma factor  &#963;24:ttgtgagcggataacaattctgaagaacaa" id="BBa_K086018" name="promoter" title="modified Lutz-Bujard LacO promoter,with alternative sigma factor  &#963;24"/>
+
-
<label for="BBa_K086018">BBa_K086018</label>
+
-
<input type="checkbox" value="BBa_K086019:modified Lutz-Bujard LacO promoter,with alternative sigma factor  &#963;24:ttgtgagcggataacaattctgataaaaca" id="BBa_K086019" name="promoter" title="modified Lutz-Bujard LacO promoter,with alternative sigma factor  &#963;24"/>
+
-
<label for="BBa_K086019">BBa_K086019</label>
+
-
<input type="checkbox" value="BBa_K086020:modified Lutz-Bujard LacO promoter,with alternative sigma factor  &#963;24 :ttgtgagcggataacatctaaccctttaga" id="BBa_K086020" name="promoter" title="modified Lutz-Bujard LacO promoter,with alternative sigma factor  &#963;24 "/>
+
-
<label for="BBa_K086020">BBa_K086020</label>
+
-
</div>
+
-
<div class="form-checkbox">
+
-
<input type="checkbox" value="BBa_K086021:modified Lutz-Bujard LacO promoter,with alternative sigma factor  &#963;24 :ttgtgagcggataacatagcagataagaaa" id="BBa_K086021" name="promoter" title="modified Lutz-Bujard LacO promoter,with alternative sigma factor  &#963;24 "/>
+
-
<label for="BBa_K086021">BBa_K086021</label>
+
-
<input type="checkbox" value="BBa_K086022:modified Lutz-Bujard LacO promoter,with alternative sigma factor  &#963;28 :gtttgagcgagtaacgccgaaaatcttgca" id="BBa_K086022" name="promoter" title="modified Lutz-Bujard LacO promoter,with alternative sigma factor  &#963;28 "/>
+
-
<label for="BBa_K086022">BBa_K086022</label>
+
-
<input type="checkbox" value="BBa_K086023:modified Lutz-Bujard LacO promoter,with alternative sigma factor  &#963;28 :gtgtgagcgagtaacgacgaaaatcttgca" id="BBa_K086023" name="promoter" title="modified Lutz-Bujard LacO promoter,with alternative sigma factor  &#963;28 "/>
+
-
<label for="BBa_K086023">BBa_K086023</label>
+
-
<input type="checkbox" value="BBa_K086024:modified Lutz-Bujard LacO promoter,with alternative sigma factor  &#963;28 :tttgagcgagtaacagccgaaaatcttgca" id="BBa_K086024" name="promoter" title="modified Lutz-Bujard LacO promoter,with alternative sigma factor  &#963;28 "/>
+
-
<label for="BBa_K086024">BBa_K086024</label>
+
-
</div>
+
-
<div class="form-checkbox">
+
-
<input type="checkbox" value="BBa_K086025:modified Lutz-Bujard LacO promoter,with alternative sigma factor  &#963;28 :tgtgagcgagtaacagccgaaaatcttgca" id="BBa_K086025" name="promoter" title="modified Lutz-Bujard LacO promoter,with alternative sigma factor  &#963;28 "/>
+
-
<label for="BBa_K086025">BBa_K086025</label>
+
-
<input type="checkbox" value="BBa_K086026:modified Lutz-Bujard LacO promoter,with alternative sigma factor  &#963;32 :ttgtgagcgagtggcaccattaagtacgta" id="BBa_K086026" name="promoter" title="modified Lutz-Bujard LacO promoter,with alternative sigma factor  &#963;32 "/>
+
-
<label for="BBa_K086026">BBa_K086026</label>
+
-
<input type="checkbox" value="BBa_K086027:modified Lutz-Bujard LacO promoter,with alternative sigma factor  &#963;32 :ttgtgagcgagtgacaccattaagtacgta" id="BBa_K086027" name="promoter" title="modified Lutz-Bujard LacO promoter,with alternative sigma factor  &#963;32 "/>
+
-
<label for="BBa_K086027">BBa_K086027</label>
+
-
<input type="checkbox" value="BBa_K086028:modified Lutz-Bujard LacO promoter,with alternative sigma factor  &#963;32 :ttgtgagcgagtaacaccattaagtacgta" id="BBa_K086028" name="promoter" title="modified Lutz-Bujard LacO promoter,with alternative sigma factor  &#963;32 "/>
+
-
<label for="BBa_K086028">BBa_K086028</label>
+
-
</div>
+
-
<div class="form-checkbox">
+
-
<input type="checkbox" value="BBa_K086029:modified Lutz-Bujard LacO promoter,with alternative sigma factor  &#963;32 :ttgtgagcgagtaacaccattaagtacgta" id="BBa_K086029" name="promoter" title="modified Lutz-Bujard LacO promoter,with alternative sigma factor  &#963;32 "/>
+
-
<label for="BBa_K086029">BBa_K086029</label>
+
-
<input type="checkbox" value="BBa_K086030:modified Lutz-Bujard LacO promoter,with alternative sigma factor  &#963;38 :cagtgagcgagtaacaactacgctgtttta" id="BBa_K086030" name="promoter" title="modified Lutz-Bujard LacO promoter,with alternative sigma factor  &#963;38 "/>
+
-
<label for="BBa_K086030">BBa_K086030</label>
+
-
<input type="checkbox" value="BBa_K086031:modified Lutz-Bujard LacO promoter,with alternative sigma factor  &#963;38 :cagtgagcgagtaacaactacgctgtttta" id="BBa_K086031" name="promoter" title="modified Lutz-Bujard LacO promoter,with alternative sigma factor  &#963;38 "/>
+
-
<label for="BBa_K086031">BBa_K086031</label>
+
-
<input type="checkbox" value="BBa_K086032:modified Lutz-Bujard LacO promoter,with alternative sigma factor  &#963;38 :atgtgagcggataacactataattaataga" id="BBa_K086032" name="promoter" title="modified Lutz-Bujard LacO promoter,with alternative sigma factor  &#963;38 "/>
+
-
<label for="BBa_K086032">BBa_K086032</label>
+
-
</div>
+
-
<div class="form-checkbox">
+
-
<input type="checkbox" value="BBa_K086033:modified Lutz-Bujard LacO promoter,with alternative sigma factor  &#963;38 :atgtgagcggataacactataattaataga" id="BBa_K086033" name="promoter" title="modified Lutz-Bujard LacO promoter,with alternative sigma factor  &#963;38 "/>
+
-
<label for="BBa_K086033">BBa_K086033</label>
+
-
</div>
+
-
<br><div class="form-checkbox">
+
-
<input type="checkbox" value="BBa_I712074:T7 promoter (strong promoter from T7 bacteriophage):agggaatacaagctacttgttctttttgca" id="BBa_I712074" name="promoter" title="T7 promoter (strong promoter from T7 bacteriophage)"/>
+
-
<label for="BBa_I712074">BBa_I712074</label>
+
-
<input type="checkbox" value="BBa_I719005:T7 Promoter:taatacgactcactatagggaga" id="BBa_I719005" name="promoter" title="T7 Promoter"/>
+
-
<label for="BBa_I719005">BBa_I719005</label>
+
-
<input type="checkbox" value="BBa_J34814:T7 Promoter:gaatttaatacgactcactatagggaga" id="BBa_J34814" name="promoter" title="T7 Promoter"/>
+
-
<label for="BBa_J34814">BBa_J34814</label>
+
-
<input type="checkbox" value="BBa_J64997:T7 consensus -10 and rest:taatacgactcactatagg" id="BBa_J64997" name="promoter" title="T7 consensus -10 and rest"/>
+
-
<label for="BBa_J64997">BBa_J64997</label>
+
-
</div>
+
-
<div class="form-checkbox">
+
-
<input type="checkbox" value="BBa_J64998:consensus -10 and rest from SP6:atttaggtgacactataga" id="BBa_J64998" name="promoter" title="consensus -10 and rest from SP6"/>
+
-
<label for="BBa_J64998">BBa_J64998</label>
+
-
<input type="checkbox" value="BBa_K113010:overlapping T7 promoter:gagtcgtattaatacgactcactatagggg" id="BBa_K113010" name="promoter" title="overlapping T7 promoter"/>
+
-
<label for="BBa_K113010">BBa_K113010</label>
+
-
<input type="checkbox" value="BBa_K113011:more overlapping T7 promoter :agtgagtcgtactacgactcactatagggg" id="BBa_K113011" name="promoter" title="more overlapping T7 promoter "/>
+
-
<label for="BBa_K113011">BBa_K113011</label>
+
-
<input type="checkbox" value="BBa_K113012:weaken overlapping T7 promoter:gagtcgtattaatacgactctctatagggg" id="BBa_K113012" name="promoter" title="weaken overlapping T7 promoter"/>
+
-
<label for="BBa_K113012">BBa_K113012</label>
+
-
</div>
+
-
<div class="form-checkbox">
+
-
<input type="checkbox" value="BBa_K525998:Promoter T7 and RBS:atacgactcactatagggaaagaggagaaa" id="BBa_K525998" name="promoter" title="Promoter T7 and RBS"/>
+
-
<label for="BBa_K525998">BBa_K525998</label>
+
-
<input type="checkbox" value="BBa_R0085:T7 Consensus Promoter Sequence:taatacgactcactatagggaga" id="BBa_R0085" name="promoter" title="T7 Consensus Promoter Sequence"/>
+
-
<label for="BBa_R0085">BBa_R0085</label>
+
-
<input type="checkbox" value="BBa_R0180:T7 RNAP promoter:ttatacgactcactatagggaga" id="BBa_R0180" name="promoter" title="T7 RNAP promoter"/>
+
-
<label for="BBa_R0180">BBa_R0180</label>
+
-
<input type="checkbox" value="BBa_R0181:T7 RNAP promoter:gaatacgactcactatagggaga" id="BBa_R0181" name="promoter" title="T7 RNAP promoter"/>
+
-
<label for="BBa_R0181">BBa_R0181</label>
+
-
</div>
+
-
<div class="form-checkbox">
+
-
<input type="checkbox" value="BBa_R0182:T7 RNAP promoter:taatacgtctcactatagggaga" id="BBa_R0182" name="promoter" title="T7 RNAP promoter"/>
+
-
<label for="BBa_R0182">BBa_R0182</label>
+
-
<input type="checkbox" value="BBa_R0183:T7 RNAP promoter:tcatacgactcactatagggaga" id="BBa_R0183" name="promoter" title="T7 RNAP promoter"/>
+
-
<label for="BBa_R0183">BBa_R0183</label>
+
-
<input type="checkbox" value="BBa_R0184:T7 promoter (lacI repressible):ataggggaattgtgagcggataacaattcc" id="BBa_R0184" name="promoter" title="T7 promoter (lacI repressible)"/>
+
-
<label for="BBa_R0184">BBa_R0184</label>
+
-
<input type="checkbox" value="BBa_R0185:T7 promoter (lacI repressible):ataggggaattgtgagcggataacaattcc" id="BBa_R0185" name="promoter" title="T7 promoter (lacI repressible)"/>
+
-
<label for="BBa_R0185">BBa_R0185</label>
+
-
</div>
+
-
<div class="form-checkbox">
+
-
<input type="checkbox" value="BBa_R0186:T7 promoter (lacI repressible):ataggggaattgtgagcggataacaattcc" id="BBa_R0186" name="promoter" title="T7 promoter (lacI repressible)"/>
+
-
<label for="BBa_R0186">BBa_R0186</label>
+
-
<input type="checkbox" value="BBa_R0187:T7 promoter (lacI repressible):ataggggaattgtgagcggataacaattcc" id="BBa_R0187" name="promoter" title="T7 promoter (lacI repressible)"/>
+
-
<label for="BBa_R0187">BBa_R0187</label>
+
-
<input type="checkbox" value="BBa_Z0251:T7 strong promoter:taatacgactcactatagggagaccacaac" id="BBa_Z0251" name="promoter" title="T7 strong promoter"/>
+
-
<label for="BBa_Z0251">BBa_Z0251</label>
+
-
<input type="checkbox" value="BBa_Z0252:T7 weak binding and processivity:taattgaactcactaaagggagaccacagc" id="BBa_Z0252" name="promoter" title="T7 weak binding and processivity"/>
+
-
<label for="BBa_Z0252">BBa_Z0252</label>
+
-
</div>
+
-
<div class="form-checkbox">
+
-
<input type="checkbox" value="BBa_Z0253:T7 weak binding promoter:cgaagtaatacgactcactattagggaaga" id="BBa_Z0253" name="promoter" title="T7 weak binding promoter"/>
+
-
<label for="BBa_Z0253">BBa_Z0253</label>
+
-
</div>
+
-
<br><div class="form-checkbox">
+
-
<input type="checkbox" value="BBa_I721001:Lead Promoter:gaaaaccttgtcaatgaagagcgatctatg" id="BBa_I721001" name="promoter" title="Lead Promoter"/>
+
-
<label for="BBa_I721001">BBa_I721001</label>
+
-
<input type="checkbox" value="BBa_I731004:FecA promoter:ttctcgttcgactcatagctgaacacaaca" id="BBa_I731004" name="promoter" title="FecA promoter"/>
+
-
<label for="BBa_I731004">BBa_I731004</label>
+
-
<input type="checkbox" value="BBa_I760005:Cu-sensitive promoter:atgacaaaattgtcat" id="BBa_I760005" name="promoter" title="Cu-sensitive promoter"/>
+
-
<label for="BBa_I760005">BBa_I760005</label>
+
-
<input type="checkbox" value="BBa_I765000:Fe promoter:accaatgctgggaacggccagggcacctaa" id="BBa_I765000" name="promoter" title="Fe promoter"/>
+
-
<label for="BBa_I765000">BBa_I765000</label>
+
-
</div>
+
-
<div class="form-checkbox">
+
-
<input type="checkbox" value="BBa_I765007:Fe and UV promoters:ctgaaagcgcataccgctatggagggggtt" id="BBa_I765007" name="promoter" title="Fe and UV promoters"/>
+
-
<label for="BBa_I765007">BBa_I765007</label>
+
-
<input type="checkbox" value="BBa_J3902:PrFe (PI + PII rus operon) :tagatatgcctgaaagcgcataccgctatg" id="BBa_J3902" name="promoter" title="PrFe (PI + PII rus operon) "/>
+
-
<label for="BBa_J3902">BBa_J3902</label>
+
-
</div>
+
-
<br><div class="form-checkbox">
+
-
<input type="checkbox" value="BBa_I1051:Lux cassette right promoter:tgttatagtcgaatacctctggcggtgata" id="BBa_I1051" name="promoter" title="Lux cassette right promoter"/>
+
-
<label for="BBa_I1051">BBa_I1051</label>
+
-
<input type="checkbox" value="BBa_I14015:P(Las) TetO:ttttggtacactccctatcagtgatagaga" id="BBa_I14015" name="promoter" title="P(Las) TetO"/>
+
-
<label for="BBa_I14015">BBa_I14015</label>
+
-
<input type="checkbox" value="BBa_I14016:P(Las) CIO:ctttttggtacactacctctggcggtgata" id="BBa_I14016" name="promoter" title="P(Las) CIO"/>
+
-
<label for="BBa_I14016">BBa_I14016</label>
+
-
<input type="checkbox" value="BBa_I14017:P(Rhl):tacgcaagaaaatggtttgttatagtcgaa" id="BBa_I14017" name="promoter" title="P(Rhl)"/>
+
-
<label for="BBa_I14017">BBa_I14017</label>
+
-
</div>
+
-
<div class="form-checkbox">
+
-
<input type="checkbox" value="BBa_I739105:Double Promoter (LuxR/HSL, positive / cI, negative):cgtgcgtgttgataacaccgtgcgtgttga" id="BBa_I739105" name="promoter" title="Double Promoter (LuxR/HSL, positive / cI, negative)"/>
+
-
<label for="BBa_I739105">BBa_I739105</label>
+
-
<input type="checkbox" value="BBa_I746104:P2 promoter in agr operon from S. aureus:agattgtactaaatcgtataatgacagtga" id="BBa_I746104" name="promoter" title="P2 promoter in agr operon from S. aureus"/>
+
-
<label for="BBa_I746104">BBa_I746104</label>
+
-
<input type="checkbox" value="BBa_I751501:plux-cI hybrid promoter:gtgttgatgcttttatcaccgccagtggta" id="BBa_I751501" name="promoter" title="plux-cI hybrid promoter"/>
+
-
<label for="BBa_I751501">BBa_I751501</label>
+
-
<input type="checkbox" value="BBa_I751502:plux-lac hybrid promoter:agtgtgtggaattgtgagcggataacaatt" id="BBa_I751502" name="promoter" title="plux-lac hybrid promoter"/>
+
-
<label for="BBa_I751502">BBa_I751502</label>
+
-
</div>
+
-
<div class="form-checkbox">
+
-
<input type="checkbox" value="BBa_I761011:CinR, CinL and glucose controlled promotor:acatcttaaaagttttagtatcatattcgt" id="BBa_I761011" name="promoter" title="CinR, CinL and glucose controlled promotor"/>
+
-
<label for="BBa_I761011">BBa_I761011</label>
+
-
<input type="checkbox" value="BBa_J06403:RhIR promoter repressible by CI:tacgcaagaaaatggtttgttatagtcgaa" id="BBa_J06403" name="promoter" title="RhIR promoter repressible by CI"/>
+
-
<label for="BBa_J06403">BBa_J06403</label>
+
-
<input type="checkbox" value="BBa_J102001:Reverse Lux Promoter:tcttgcgtaaacctgtacgatcctacaggt" id="BBa_J102001" name="promoter" title="Reverse Lux Promoter"/>
+
-
<label for="BBa_J102001">BBa_J102001</label>
+
-
<input type="checkbox" value="BBa_J64000:rhlI promoter:atcctcctttagtcttccccctcatgtgtg" id="BBa_J64000" name="promoter" title="rhlI promoter"/>
+
-
<label for="BBa_J64000">BBa_J64000</label>
+
-
</div>
+
-
<div class="form-checkbox">
+
-
<input type="checkbox" value="BBa_J64010:lasI promoter:taaaattatgaaatttgcataaattcttca" id="BBa_J64010" name="promoter" title="lasI promoter"/>
+
-
<label for="BBa_J64010">BBa_J64010</label>
+
-
<input type="checkbox" value="BBa_J64067:LuxR+3OC6HSL independent R0065:gtgttgactattttacctctggcggtgata" id="BBa_J64067" name="promoter" title="LuxR+3OC6HSL independent R0065"/>
+
-
<label for="BBa_J64067">BBa_J64067</label>
+
-
<input type="checkbox" value="BBa_J64712:LasR/LasI Inducible &amp; RHLR/RHLI repressible Promoter:gaaatctggcagtttttggtacacgaaagc" id="BBa_J64712" name="promoter" title="LasR/LasI Inducible &amp; RHLR/RHLI repressible Promoter"/>
+
-
<label for="BBa_J64712">BBa_J64712</label>
+
-
<input type="checkbox" value="BBa_K091107:pLux/cI Hybrid Promoter:acaccgtgcgtgttgatatagtcgaataaa" id="BBa_K091107" name="promoter" title="pLux/cI Hybrid Promoter"/>
+
-
<label for="BBa_K091107">BBa_K091107</label>
+
-
</div>
+
-
<div class="form-checkbox">
+
-
<input type="checkbox" value="BBa_K091117:pLas promoter:aaaattatgaaatttgtataaattcttcag" id="BBa_K091117" name="promoter" title="pLas promoter"/>
+
-
<label for="BBa_K091117">BBa_K091117</label>
+
-
<input type="checkbox" value="BBa_K091143:pLas/cI Hybrid Promoter:ggttctttttggtacctctggcggtgataa" id="BBa_K091143" name="promoter" title="pLas/cI Hybrid Promoter"/>
+
-
<label for="BBa_K091143">BBa_K091143</label>
+
-
<input type="checkbox" value="BBa_K091146:pLas/Lux Hybrid Promoter:tgtaggatcgtacaggtataaattcttcag" id="BBa_K091146" name="promoter" title="pLas/Lux Hybrid Promoter"/>
+
-
<label for="BBa_K091146">BBa_K091146</label>
+
-
<input type="checkbox" value="BBa_K091156:pLux:caagaaaatggtttgttatagtcgaataaa" id="BBa_K091156" name="promoter" title="pLux"/>
+
-
<label for="BBa_K091156">BBa_K091156</label>
+
-
</div>
+
-
<div class="form-checkbox">
+
-
<input type="checkbox" value="BBa_K091157:pLux/Las Hybrid Promoter:ctatctcatttgctagtatagtcgaataaa" id="BBa_K091157" name="promoter" title="pLux/Las Hybrid Promoter"/>
+
-
<label for="BBa_K091157">BBa_K091157</label>
+
-
<input type="checkbox" value="BBa_K145150:Hybrid promoter: HSL-LuxR activated, P22 C2 repressed:tagtttataatttaagtgttctttaatttc" id="BBa_K145150" name="promoter" title="Hybrid promoter: HSL-LuxR activated, P22 C2 repressed"/>
+
-
<label for="BBa_K145150">BBa_K145150</label>
+
-
<input type="checkbox" value="BBa_K266000:PAI+LasR -:caccttcgggtgggcctttctgcgtttata" id="BBa_K266000" name="promoter" title="PAI+LasR -"/>
+
-
<label for="BBa_K266000">BBa_K266000</label>
+
-
<input type="checkbox" value="BBa_K266005:PAI+LasR -:aataactctgatagtgctagtgtagatctc" id="BBa_K266005" name="promoter" title="PAI+LasR -"/>
+
-
<label for="BBa_K266005">BBa_K266005</label>
+
-
</div>
+
-
<div class="form-checkbox">
+
-
<input type="checkbox" value="BBa_K266006:PAI+LasR -:caccttcgggtgggcctttctgcgtttata" id="BBa_K266006" name="promoter" title="PAI+LasR -"/>
+
-
<label for="BBa_K266006">BBa_K266006</label>
+
-
<input type="checkbox" value="BBa_K266007:Complex QS -:caccttcgggtgggcctttctgcgtttata" id="BBa_K266007" name="promoter" title="Complex QS -"/>
+
-
<label for="BBa_K266007">BBa_K266007</label>
+
-
<input type="checkbox" value="BBa_K658006:position 3 mutated promoter lux pR-3 (luxR &amp; HSL regulated):caagaaaatggtttgttatagtcgaataaa" id="BBa_K658006" name="promoter" title="position 3 mutated promoter lux pR-3 (luxR &amp; HSL regulated)"/>
+
-
<label for="BBa_K658006">BBa_K658006</label>
+
-
<input type="checkbox" value="BBa_K658007:position 5 mutated promoter lux pR-5 (luxR &amp; HSL regulated) :caagaaaatggtttgttatagtcgaataaa" id="BBa_K658007" name="promoter" title="position 5 mutated promoter lux pR-5 (luxR &amp; HSL regulated) "/>
+
-
<label for="BBa_K658007">BBa_K658007</label>
+
-
</div>
+
-
<div class="form-checkbox">
+
-
<input type="checkbox" value="BBa_K658008:position 3&amp;5 mutated promoter lux pR-3/5 (luxR &amp; HSL regulated):caagaaaatggtttgttatagtcgaataaa" id="BBa_K658008" name="promoter" title="position 3&amp;5 mutated promoter lux pR-3/5 (luxR &amp; HSL regulated)"/>
+
-
<label for="BBa_K658008">BBa_K658008</label>
+
-
<input type="checkbox" value="BBa_R0061:Promoter (HSL-mediated luxR repressor):ttgacacctgtaggatcgtacaggtataat" id="BBa_R0061" name="promoter" title="Promoter (HSL-mediated luxR repressor)"/>
+
-
<label for="BBa_R0061">BBa_R0061</label>
+
-
<input type="checkbox" value="BBa_R0062:Promoter (luxR &amp; HSL regulated -- lux pR):caagaaaatggtttgttatagtcgaataaa" id="BBa_R0062" name="promoter" title="Promoter (luxR &amp; HSL regulated -- lux pR)"/>
+
-
<label for="BBa_R0062">BBa_R0062</label>
+
-
<input type="checkbox" value="BBa_R0063:Promoter (luxR &amp; HSL regulated -- lux pL):cacgcaaaacttgcgacaaacaataggtaa" id="BBa_R0063" name="promoter" title="Promoter (luxR &amp; HSL regulated -- lux pL)"/>
+
-
<label for="BBa_R0063">BBa_R0063</label>
+
-
</div>
+
-
<div class="form-checkbox">
+
-
<input type="checkbox" value="BBa_R0071:Promoter (RhlR &amp; C4-HSL regulated):gttagctttcgaattggctaaaaagtgttc" id="BBa_R0071" name="promoter" title="Promoter (RhlR &amp; C4-HSL regulated)"/>
+
-
<label for="BBa_R0071">BBa_R0071</label>
+
-
<input type="checkbox" value="BBa_R0078:Promoter (cinR and HSL regulated):ccattctgctttccacgaacttgaaaacgc" id="BBa_R0078" name="promoter" title="Promoter (cinR and HSL regulated)"/>
+
-
<label for="BBa_R0078">BBa_R0078</label>
+
-
<input type="checkbox" value="BBa_R0079:Promoter (LasR &amp; PAI regulated):ggccgcgggttctttttggtacacgaaagc" id="BBa_R0079" name="promoter" title="Promoter (LasR &amp; PAI regulated)"/>
+
-
<label for="BBa_R0079">BBa_R0079</label>
+
-
<input type="checkbox" value="BBa_R1062:Promoter, Standard (luxR and HSL regulated -- lux pR):aagaaaatggtttgttgatactcgaataaa" id="BBa_R1062" name="promoter" title="Promoter, Standard (luxR and HSL regulated -- lux pR)"/>
+
-
<label for="BBa_R1062">BBa_R1062</label>
+
-
</div>
+
-
<br>
+
-
<br>
+
-
<br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br>
+
-
<input type=BUTTON value="Submit" name="mySubmit" onClick="setup()"></form>
+
-
</p>
+
-
<div id="visualizationButtons"></div>
+
-
<div id="readout"></div>
+
-
<div id="infovis"></div>
+
-
<div id="inner-details"></div>
+
-
</body>
+
</html>
</html>
 +
{{Team:Amsterdam/Foot}}

Latest revision as of 22:41, 26 September 2012

Retrieved from "http://2012.igem.org/Team:Amsterdam/maarten/"