Team:Freiburg/Project/modeling/crRNA/js

From 2013.igem.org

(Difference between revisions)
 
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   }
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   }
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var oligo2rev = oligo1.slice();
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for( var k=0; k<oligo1.length; k++ ) {
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  oligo2rev[k] = oligo2[k].split("").reverse().join("");
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}
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w.document.writeln("<h3> Oligo number: " + (parseInt(i, 10) + parseInt(1, 10)) + " was found at position " + (parseInt(index[i], 10) + parseInt(1, 10))  + "</h3>");
w.document.writeln("<h3> Oligo number: " + (parseInt(i, 10) + parseInt(1, 10)) + " was found at position " + (parseInt(index[i], 10) + parseInt(1, 10))  + "</h3>");
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     w.document.writeln("<p>Oligo1: " + oligo1[i] + "</p><p>Oligo2: " + oligo2[i] + "</p>");
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     w.document.writeln("<p>Oligo1: " + oligo1[i] + "</p><p>Oligo2: " + oligo2[i] + "</p>");
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     w.document.writeln("<pre>Oligo1: " + oligo1[i] + "<br>           ||||||||||||||||||||||||||||||||<br>Oligo2:   " +  
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     w.document.writeln("<pre>Oligo1: " + oligo1[i] + "<br>           ||||||||||||||||||||||||||||||||<br>Oligo2:     " +  
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oligo2[i].split('').reverse().join('') + "</pre>");
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oligo2rev[i] + "</pre>");
    
    
     }
     }
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alert('Working.');   
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w.document.writeln("</td>");
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}
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} );
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</script>
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<SCRIPT LANGUAGE="JavaScript">
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function CrispR (form) {
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  TestVar = TestVar.replace(/</g,"\n <");
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  var w = window.open("blank.html", "blank", "height=50,width=300");
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  w.document.writeln("<h2> The inserted sequence is: </h2>");
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  w.document.writeln(TestVar);
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    w.document.writeln("<h1>possible crRNAs are:</h1><div>");
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  w.document.writeln("<table>");
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    w.document.writeln("<tr><td>");
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    for (i=0; i<oligo2.length; i++ ) {
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    w.document.writeln("<h3> Oligo number: " + (parseInt(i, 10) + parseInt(1, 10)) + " was found at position " +
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(parseInt(index[i], 10) + parseInt(1, 10))  + "</h3>");
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    w.document.writeln("<p>Oligo1: " + oligo1[i] + "</p><p>Oligo2: " + oligo2[i] + "</p>");
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    w.document.writeln("<pre>Oligo1: " + oligo1[i] + "<br>
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&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;||||||||||||||||||||||||||||||||<br>Oligo2: &nbsp;&nbsp;&nbsp;&nbsp;" +
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oligo2[i].split("").reverse().join("") + "</pre>");
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    }
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  w.document.writeln("</td>");
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   w.document.writeln("<td>");
   w.document.writeln("<td>");
    
    
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   w.document.writeln("</div>");
   w.document.writeln("</div>");
  
  
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   w.document.close();
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   w.document.close();  
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}
}
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</SCRIPT>
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} );
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</script>
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<style type="text/css">
<style type="text/css">
body {  
body {  

Latest revision as of 22:22, 26 September 2013

CrispR

button

crRNA-Design

Enter Target Sequence

Choose Program

Which strand should be targeted?

non coding strand coding strand

This tool helps you to design a crRNA-insert for pX334a. The oligos contain overhangs which fit to the BbsI-overhangs by pX334a.

For repression of gene transcription by targeting the coding sequence it´s crucial to target the non template (= coding) DNA strand.
Therefore the oligos must be designed as follows:

  1. Search at your desired target sequence for a CCN (reverse complement of the PAM sequence) at the coding strand.
  2. Extract the following (3') 30 nucleotides.
  3. Extract the reverse complement.
  4. Add AAAC at the 5' end and GT at the 3' end. This will be your fist oligo.
  5. Take the sequence from step 2 and add TAAAAC at the 5' end. This will be your second oligo.

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