Team:HokkaidoU Japan/Shuffling Kit/Primer Designer

From 2013.igem.org

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   <div id="common-header-bottom-background">
   <div id="common-header-bottom-background">
     <div class="wrapper">
     <div class="wrapper">
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       <h1 id="common-header-title">Maestro E.coli</h1>
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       <h1 id="common-header-title">Maestro <span class="italic">E. coli</span></h1>
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       <h2 id="common-header-subtitle">Optimization Kit</h2>
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       <h2 id="common-header-subtitle">Shuffling Kit</h2>
       <img id="common-header-img" src="https://static.igem.org/mediawiki/2013/e/ea/HokkaidoU2013_Maestro_Header.png">
       <img id="common-header-img" src="https://static.igem.org/mediawiki/2013/e/ea/HokkaidoU2013_Maestro_Header.png">
     </div>
     </div>
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     <div id="hokkaidou-contents">
     <div id="hokkaidou-contents">
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ul{list-style:none;margin-left:0}#plasmid-map{width:100%;height:160px}#plasmid-map div{position:relative;float:left;height:100%;background:url("https://static.igem.org/mediawiki/2013/4/4d/HokkaidoU2013_Plasmid_Parts.png") no-repeat}#plasmid-map #plasmid-0{width:80px}#plasmid-map #plasmid-1{width:101px}#plasmid-map #plasmid-2{width:83px}#plasmid-map #plasmid-3{width:99px}#plasmid-map #plasmid-4{width:83px}#plasmid-map #plasmid-5{width:99px}#plasmid-map #plasmid-6{width:83px}#plasmid-map #plasmid-7{width:99px}#plasmid-map #plasmid-8{width:73px}#plasmid-map #plasmid-9{width:80px}#plasmid-map #plasmid-0{background-position:0 -160px}#plasmid-map #plasmid-1{background-position:-81px -160px}#plasmid-map #plasmid-2{background-position:-184px -160px}#plasmid-map #plasmid-3{background-position:-269px -160px}#plasmid-map #plasmid-4{background-position:-184px -160px}#plasmid-map #plasmid-5{background-position:-269px -160px}#plasmid-map #plasmid-6{background-position:-184px -160px}#plasmid-map #plasmid-7{background-position:-269px -160px}#plasmid-map #plasmid-8{background-position:-369px -160px}#plasmid-map #plasmid-9{background-position:-442px -160px}#plasmid-map #plasmid-0.plasmid-gray{background-position:0 0}#plasmid-map #plasmid-1.plasmid-gray{background-position:-81px 0}#plasmid-map #plasmid-2.plasmid-gray{background-position:-184px 0}#plasmid-map #plasmid-3.plasmid-gray{background-position:-269px 0}#plasmid-map #plasmid-4.plasmid-gray{background-position:-184px 0}#plasmid-map #plasmid-5.plasmid-gray{background-position:-269px 0}#plasmid-map #plasmid-6.plasmid-gray{background-position:-184px 0}#plasmid-map #plasmid-7.plasmid-gray{background-position:-269px 0}#plasmid-map #plasmid-8.plasmid-gray{background-position:-369px 0}#plasmid-map #plasmid-9.plasmid-gray{background-position:-442px 0}#plasmid-map span{position:absolute;top:40px;left:-5px}.my-form{width:100%}.my-form label{width:300px;text-align:right}textarea{width:500px}.monospace{font-family:'Inconsolata'!important;font-size:18px!important}option[disabled]{color:#c6c6c6}input[type="radio"]{padding:0}textarea{overflow:auto;vertical-align:top}label{display:inline-block;margin-bottom:5px}input[type="radio"],input[type="checkbox"]{margin:4px 0 0;margin-top:1px \9;line-height:normal}input[type="file"]:focus,input[type="radio"]:focus,input[type="checkbox"]:focus{outline:thin dotted #333;outline:5px auto -webkit-focus-ring-color;outline-offset:-2px}.form-control{font-family:'Open Sans';padding:6px 12px;font-size:14px;line-height:1.428571429;color:#555;vertical-align:middle;background-color:#fff;border:1px solid #ccc;border-radius:4px;-webkit-box-shadow:inset 0 1px 1px rgba(0,0,0,0.075);box-shadow:inset 0 1px 1px rgba(0,0,0,0.075);-webkit-transition:border-color ease-in-out .15s,box-shadow ease-in-out .15s;transition:border-color ease-in-out .15s,box-shadow ease-in-out .15s}.form-control[disabled],.form-control[readonly],fieldset[disabled] .form-control{cursor:not-allowed;background-color:#eee}textarea.form-control{height:auto}.form-group{margin-bottom:15px}.radio,.checkbox{display:block;min-height:20px;margin-top:10px;margin-bottom:10px;padding-left:20px;vertical-align:middle}.radio label,.checkbox label{display:inline;margin-bottom:0;font-weight:normal;cursor:pointer}.radio input[type="radio"],.radio-inline input[type="radio"],.checkbox input[type="checkbox"],.checkbox-inline input[type="checkbox"]{float:left;margin-left:-20px}.radio+.radio,.checkbox+.checkbox{margin-top:-5px}
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</style>
<!-- end header / begin contents -->
<!-- end header / begin contents -->
<link href='http://fonts.googleapis.com/css?family=Inconsolata' rel='stylesheet' type='text/css'>
<link href='http://fonts.googleapis.com/css?family=Inconsolata' rel='stylesheet' type='text/css'>
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             <h1>GGA Primer Designer</h1>
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             <h1>Primer Designer for Maestro</h1>
             <h3>1. First, you have to decide whether or not you conform to our default overhang set.</h3>
             <h3>1. First, you have to decide whether or not you conform to our default overhang set.</h3>
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               CDS(s) included.
               CDS(s) included.
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               <h3>3. Then, please select the region to where your biobrick correspond in target plasmid.</h3>
+
               <h3>3. Then, please select the region to where your fragment correspond in target plasmid.</h3>
               <div id="plasmid-map">
               <div id="plasmid-map">
                 <div                            id="plasmid-0">                                  </div>
                 <div                            id="plasmid-0">                                  </div>
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                 <div class="form-group">
                 <div class="form-group">
                   <label for="part-beginning">
                   <label for="part-beginning">
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                     Beginning of the Biobrick:
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                     Beginning of the fragment:
                   </label>
                   </label>
                   <select name="part-beginning" class="form-control monospace">
                   <select name="part-beginning" class="form-control monospace">
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                 <div class="form-group">
                 <div class="form-group">
                   <label for="part-end">
                   <label for="part-end">
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                     End of the Biobrick:
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                     End of the fragment:
                   </label>
                   </label>
                   <select name="part-end" class="form-control monospace">
                   <select name="part-end" class="form-control monospace">
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               <h3>4. Okey, now we are ready to go. Enter your biobrick's sequence, and press "Calculate"!</h3>
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               <h3>4. Okey, now we are ready to go. Enter your fragment's sequence, and press "Calculate"!</h3>
             </div>
             </div>
             <div id="not-conform">
             <div id="not-conform">
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               <h3>2. Please enter overhangs and biobrick's sequence, and press "Calculate"</h3>
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               <h3>2. Please enter overhangs and fragment's sequence, and press "Calculate"</h3>
             </div>
             </div>
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               <div class="form-group">
               <div class="form-group">
                 <label for="sequence">
                 <label for="sequence">
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                   Biobrick sequence:
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                   Fragment sequence:
                 </label>
                 </label>
               <textarea class="form-control monospace" type="text" name="sequence"></textarea><br>
               <textarea class="form-control monospace" type="text" name="sequence"></textarea><br>
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             </dl>
             </dl>
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             <h3>5. Now, repeat previous step for remaining biobricks included in the target plasmid.</h3>
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             <h3>5. Now, repeat previous step for remaining fragments included in the target plasmid.</h3>
<script type="text/javascript">
<script type="text/javascript">
-
(function(){var n,e,g,h,d,a,j,f,i,b,m,k,c,l;a=function(o){switch(o){case"AA":case"TT":return -9.1;case"AT":return -8.6;case"TA":return -6;case"CA":case"TG":return -5.8;case"GT":case"AC":return -6.5;case"CT":case"AG":return -7.8;case"GA":case"TC":return -5.6;case"CG":return -11.9;case"GC":return -11.1;case"GG":case"CC":return -11}};k=function(o){var p,q,s,r;q=0;for(p=s=0,r=o.length-2;0<=r?s<=r:s>=r;p=0<=r?++s:--s){q+=a(o.slice(p,+(p+1)+1||9000000000))}return q};j=function(o){switch(o){case"AA":case"TT":return -24;case"AT":return -23.9;case"TA":return -16.9;case"CA":case"TG":return -12.9;case"GT":case"AC":return -17.3;case"CT":case"AG":return -20.8;case"GA":case"TC":return -13.5;case"CG":return -27.8;case"GC":return -26.7;case"GG":case"CC":return -26.6}};c=function(o){var p,q,s,r;q=0;for(p=s=0,r=o.length-2;0<=r?s<=r:s>=r;p=0<=r?++s:--s){q+=j(o.slice(p,+(p+1)+1||9000000000))}return q};n=function(o){var q,p;q=k(o);p=c(o);return(1000*q/(-10.8+p+1.987*-15.89495209964411))-273.15+16.6*-1.3010299956639813};d=function(p){var r,o,q;if(n(p.slice(0,35))<60){alert("Sequence is too short.");return false}for(r=q=17;q<=35;r=++q){o=n(p.slice(0,+(r-1)+1||9000000000));if(o>60){if(p[r-1]==="G"||p[r-1]==="C"){break}}}return[p.slice(0,+(r-1)+1||9000000000),o]};h=function(o){switch(o){case"A":return"T";case"T":return"A";case"G":return"C";case"C":return"G"}};m=function(p){var o;return((function(){var t,r,s,q;s=p.split("");q=[];for(t=0,r=s.length;t<r;t++){o=s[t];q.push(h(o))}return q})()).reverse().join("")};f=function(s,o,w){var t,p,r,u,v,q;t=d(w);p=d(m(w));r="TTTGGTCTCT"+s+"T"+t[0];v=t[1];u="TTTGGTCTCA"+o+"A"+p[0];q=p[1];return[r,v,u,q]};g=function(o){if(/GGTCTC/.test(o)||/GGTCTC/.test(m(o))){return false}else{return true}};e=function(p){var o;o=/[ATCG]+/.exec(p);console.log(o);if(o[0]===p){return true}else{return false}};b=function(p){var o;o=p.val().toUpperCase().split(/[\s\n\r]+/).join("");if(!e(o)){alert("You can NOT use non-AGCT characters.");p.focus();return false}if(!g(o)){alert("This sequence contains BsaI cutting site.");p.focus();return false}};i=function(o){switch(o){case 1:return"CGTC";case 2:return"AAGG";case 3:return"CTGA";case 4:return"TTAT";case 5:return"TTCG";case 6:return"TAGA";case 7:return"TCCC";case 8:return"CGGT";case 9:return"AGTA"}};l=function(){var t,o,p,s,r,q;t=parseInt($('[name="part-beginning"]').val());o=parseInt($('[name="part-end"]').val());for(p=s=1;1<=t?s<t:s>t;p=1<=t?++s:--s){$("#plasmid-"+p).addClass("plasmid-gray")}for(p=r=t;t<=9?r<=9:r>=9;p=t<=9?++r:--r){$("#plasmid-"+p).removeClass("plasmid-gray")}for(p=q=o;o<=9?q<=9:q>=9;p=o<=9?++q:--q){$("#plasmid-"+p).addClass("plasmid-gray")}if(o>t){$('[name="overhang-f"]').val(i(t));return $('[name="overhang-r"]').val(i(o))}else{$('[name="overhang-f"]').val("");return $('[name="overhang-r"]').val("")}};$(function(){$('[name="overhang-f"]').focusout(function(){return b($(this))});$('[name="overhang-r"]').focusout(function(){return b($(this))});$('[name="sequence"]').focusout(function(){return b($(this))});$("#primer-designer").submit(function(r){var q,p,u,s,o,t;r.preventDefault();p=$(this);q=p.find("button");q.attr("disabled",true);u=p.find('[name="overhang-f"]').val().toUpperCase();s=p.find('[name="overhang-r"]').val().toUpperCase();t=p.find('[name="sequence"]').val().toUpperCase().split(/[\s\n\r]+/).join("");console.log(g(u));console.log(g(s));console.log(g(t));console.log(e(u));console.log(e(s));console.log(e(t));o=f(u,m(s),t);$("#primer-f").text(o[0]);$("#tm-f").html(""+(o[1].toFixed(2))+" &deg;C");$("#primer-r").text(o[2]);$("#tm-r").html(""+(o[3].toFixed(2))+" &deg;C");return q.attr("disabled",false)});$("#not-conform").hide();$('input[name="default"]:radio').change(function(){switch($(this).val()){case"1":$("#conform").show();return $("#not-conform").hide();case"2":$("#conform").hide();return $("#not-conform").show()}});$('[name="cds-number"]').val("3");$('[name="cds-number"]').change(function(){switch($(this).val()){case"1":$(".hide-1").hide();$(".hide-2").hide();$(".disable-1").attr("disabled","disabled");return $(".disable-2").attr("disabled","disabled");case"2":$(".hide-1").show();$(".hide-2").hide();$(".disable-1").removeAttr("disabled");return $(".disable-2").attr("disabled","disabled");case"3":$(".hide-1").show();$(".hide-2").show();$(".disable-1").removeAttr("disabled");return $(".disable-2").removeAttr("disabled")}});$('[name="part-beginning"]').change(function(){return l()});return $('[name="part-end"]').change(function(){return l()})})}).call(this);
+
(function(){var n,f,e,h,d,a,j,g,i,b,m,k,c,l;a=function(o){switch(o){case"AA":case"TT":return -9.1;case"AT":return -8.6;case"TA":return -6;case"CA":case"TG":return -5.8;case"GT":case"AC":return -6.5;case"CT":case"AG":return -7.8;case"GA":case"TC":return -5.6;case"CG":return -11.9;case"GC":return -11.1;case"GG":case"CC":return -11}};k=function(o){var p,q,s,r;q=0;for(p=s=0,r=o.length-2;0<=r?s<=r:s>=r;p=0<=r?++s:--s){q+=a(o.slice(p,+(p+1)+1||9000000000))}return q};j=function(o){switch(o){case"AA":case"TT":return -24;case"AT":return -23.9;case"TA":return -16.9;case"CA":case"TG":return -12.9;case"GT":case"AC":return -17.3;case"CT":case"AG":return -20.8;case"GA":case"TC":return -13.5;case"CG":return -27.8;case"GC":return -26.7;case"GG":case"CC":return -26.6}};c=function(o){var p,q,s,r;q=0;for(p=s=0,r=o.length-2;0<=r?s<=r:s>=r;p=0<=r?++s:--s){q+=j(o.slice(p,+(p+1)+1||9000000000))}return q};n=function(o){var q,p;q=k(o);p=c(o);return(1000*q/(-10.8+p+1.987*-15.89495209964411))-273.15+16.6*-1.3010299956639813};d=function(p){var r,o,q;if(n(p.slice(0,35))<60){alert("Sequence is too short.");return false}for(r=q=17;q<=35;r=++q){o=n(p.slice(0,+(r-1)+1||9000000000));if(o>60){if(p[r-1]==="G"||p[r-1]==="C"){break}}}return[p.slice(0,+(r-1)+1||9000000000),o]};h=function(o){switch(o){case"A":return"T";case"T":return"A";case"G":return"C";case"C":return"G"}};m=function(p){var o;return((function(){var t,r,s,q;s=p.split("");q=[];for(t=0,r=s.length;t<r;t++){o=s[t];q.push(h(o))}return q})()).reverse().join("")};g=function(s,o,w){var t,p,r,u,v,q;t=d(w);p=d(m(w));r="TTTGGTCTCT"+s+"T"+t[0];v=t[1];u="TTTGGTCTCA"+o+"A"+p[0];q=p[1];return[r,v,u,q]};e=function(p){var o;o=true;if(/GGTCTC/.test(p)||/GGTCTC/.test(m(p))){alert('This sequence contains BsaI cutting site "GGTCTC" or "GAGACC".\r\nYou can just ignore this alert, if unnecessary.');o=false}if(/GAATTC/.test(p)||/GAATTC/.test(m(p))){alert('This sequence contains EcoRI cutting site "GAATTC".\r\nYou can just ignore this alert, if unnecessary.');o=false}if(/CTGCAG/.test(p)||/CTGCAG/.test(m(p))){alert('This sequence contains PstI cutting site "CTGCAG".\r\nYou can just ignore this alert, if unnecessary.');o=false}if(/GCGGCCGC/.test(p)||/GCGGCCGC/.test(m(p))){alert('This sequence contains NotI cutting site "GCGGCCGC".\r\nYou can just ignore this alert, if unnecessary.');o=false}if(/ACTAGT/.test(p)||/ACTAGT/.test(m(p))){alert('This sequence contains SpeI cutting site "ACTAGT".\r\nYou can just ignore this alert, if unnecessary.');o=false}if(/TCTAGA/.test(p)||/TCTAGA/.test(m(p))){alert('This sequence contains XbaI cutting site "TCTAGA".\r\nYou can just ignore this alert, if unnecessary.');o=false}return o};f=function(p){var o;o=/[ATCG]+/.exec(p);if(o[0]===p){return true}else{return false}};b=function(p){var o;o=p.val().toUpperCase().split(/[\s\n\r]+/).join("");if(!f(o)){alert("You can NOT use non-AGCT characters.");return false}if(!e(o)){return false}};i=function(o){switch(o){case 1:return"CGTC";case 2:return"AAGG";case 3:return"CTGA";case 4:return"TTAT";case 5:return"TTCG";case 6:return"TAGA";case 7:return"TCCC";case 8:return"CGGT";case 9:return"AGTA"}};l=function(){var t,o,p,s,r,q;t=parseInt($('[name="part-beginning"]').val());o=parseInt($('[name="part-end"]').val());for(p=s=1;1<=t?s<t:s>t;p=1<=t?++s:--s){$("#plasmid-"+p).addClass("plasmid-gray")}for(p=r=t;t<=9?r<=9:r>=9;p=t<=9?++r:--r){$("#plasmid-"+p).removeClass("plasmid-gray")}for(p=q=o;o<=9?q<=9:q>=9;p=o<=9?++q:--q){$("#plasmid-"+p).addClass("plasmid-gray")}if(o>t){$('[name="overhang-f"]').val(i(t));return $('[name="overhang-r"]').val(i(o))}else{$('[name="overhang-f"]').val("");return $('[name="overhang-r"]').val("")}};$(function(){$('[name="overhang-f"]').focusout(function(){return b($(this))});$('[name="overhang-r"]').focusout(function(){return b($(this))});$('[name="sequence"]').focusout(function(){return b($(this))});$("#primer-designer").submit(function(r){var q,p,u,s,o,t;r.preventDefault();p=$(this);q=p.find("button");q.attr("disabled",true);u=p.find('[name="overhang-f"]').val().toUpperCase();s=p.find('[name="overhang-r"]').val().toUpperCase();t=p.find('[name="sequence"]').val().toUpperCase().split(/[\s\n\r]+/).join("");o=g(u,m(s),t);$("#primer-f").text(o[0]);$("#tm-f").html(""+(o[1].toFixed(2))+" &deg;C");$("#primer-r").text(o[2]);$("#tm-r").html(""+(o[3].toFixed(2))+" &deg;C");return q.attr("disabled",false)});$("#not-conform").hide();$('input[name="default"]:radio').change(function(){switch($(this).val()){case"1":$("#conform").show();return $("#not-conform").hide();case"2":$("#conform").hide();return $("#not-conform").show()}});$('[name="cds-number"]').val("3");$('[name="cds-number"]').change(function(){switch($(this).val()){case"1":$(".hide-1").hide();$(".hide-2").hide();$(".disable-1").attr("disabled","disabled");return $(".disable-2").attr("disabled","disabled");case"2":$(".hide-1").show();$(".hide-2").hide();$(".disable-1").removeAttr("disabled");return $(".disable-2").attr("disabled","disabled");case"3":$(".hide-1").show();$(".hide-2").show();$(".disable-1").removeAttr("disabled");return $(".disable-2").removeAttr("disabled")}});$('[name="part-beginning"]').change(function(){return l()});return $('[name="part-end"]').change(function(){return l()})})}).call(this);
</script>
</script>
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Latest revision as of 02:50, 29 October 2013

Maestro E. coli

Shuffling Kit

Primer Designer for Maestro

1. First, you have to decide whether or not you conform to our default overhang set.

2. Secondly, you hove to determine how many CDS are included in your target plasmid.

I have CDS(s) included.

3. Then, please select the region to where your fragment correspond in target plasmid.

1
2
3
4
5
6
7
8
9

4. Okey, now we are ready to go. Enter your fragment's sequence, and press "Calculate"!

2. Please enter overhangs and fragment's sequence, and press "Calculate"





Forward

sequence
tm

Reverse

sequence
tm

5. Now, repeat previous step for remaining fragments included in the target plasmid.