Team:HokkaidoU Japan/Shuffling Kit/Primer Designer

From 2013.igem.org

(Difference between revisions)
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(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(o){if(/GGTCTC/.test(o)||/GGTCTC/.test(m(o))){alert("This sequence contains BsaI cutting site.");return false}else{if(/GAATTC/.test(o)||/GAATTC/.test(m(o))){alert("This sequence contains EcoRI cutting site.");return false}else{if(/CTGCAG/.test(o)||/CTGCAG/.test(m(o))){alert("This sequence contains PstI cutting site.");return false}else{if(/GCGGCCGC/.test(o)||/GCGGCCGC/.test(m(o))){alert("This sequence contains NotI cutting site.");return false}else{if(/ACTAGT/.test(o)||/ACTAGT/.test(m(o))){alert("This sequence contains SpeI cutting site.");return false}else{if(/TCTAGA/.test(o)||/TCTAGA/.test(m(o))){alert("This sequence contains XbaI cutting site.");return false}else{return true}}}}}}};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("");console.log(check_bsa_site(u));console.log(check_bsa_site(s));console.log(check_bsa_site(t));console.log(f(u));console.log(f(s));console.log(f(t));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);
(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(o){if(/GGTCTC/.test(o)||/GGTCTC/.test(m(o))){alert("This sequence contains BsaI cutting site.");return false}else{if(/GAATTC/.test(o)||/GAATTC/.test(m(o))){alert("This sequence contains EcoRI cutting site.");return false}else{if(/CTGCAG/.test(o)||/CTGCAG/.test(m(o))){alert("This sequence contains PstI cutting site.");return false}else{if(/GCGGCCGC/.test(o)||/GCGGCCGC/.test(m(o))){alert("This sequence contains NotI cutting site.");return false}else{if(/ACTAGT/.test(o)||/ACTAGT/.test(m(o))){alert("This sequence contains SpeI cutting site.");return false}else{if(/TCTAGA/.test(o)||/TCTAGA/.test(m(o))){alert("This sequence contains XbaI cutting site.");return false}else{return true}}}}}}};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("");console.log(check_bsa_site(u));console.log(check_bsa_site(s));console.log(check_bsa_site(t));console.log(f(u));console.log(f(s));console.log(f(t));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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Revision as of 00:28, 28 September 2013

Maestro E.coli

Optimization Kit

POK-ROK Primer Designer

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 flagment correspond in target plasmid.

1
2
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9

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

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




Forward

sequence

              
tm

              

            

            
Reverse

            

              
sequence

              

              
tm

              

            


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






How To Use






Examples




    

  



  





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