Team:Freiburg/Project/modeling/crRNA/js
From 2013.igem.org
(Difference between revisions)
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+ | |||
<html> | <html> | ||
+ | <head> | ||
+ | <title>CrispR</title> | ||
+ | <link rel="stylesheet" type="text/css"> | ||
+ | <script type="text/javascript" src="script.js"></script> | ||
<SCRIPT LANGUAGE="JavaScript"> | <SCRIPT LANGUAGE="JavaScript"> | ||
- | function CrispR(form) { | + | function CrispR (form) { |
var TestVar = form.Sequenz.value; | var TestVar = form.Sequenz.value; | ||
var length = TestVar.length; | var length = TestVar.length; | ||
Line 77: | Line 82: | ||
var j = 0; | var j = 0; | ||
for( var k=0; k<oligo2.length; k++ ) { | for( var k=0; k<oligo2.length; k++ ) { | ||
- | TestVar = TestVar.substring(0,index[k]+30+j) + TestVar.substring(index[k]+30+j,index[k]+33+j).fontcolor("red") + TestVar.substring(index[k]+33+j,TestVar.length); | + | TestVar = TestVar.substring(0,index[k]+30+j) + TestVar.substring(index[k]+30+j,index[k]+33+j).fontcolor("red") + |
+ | |||
+ | TestVar.substring(index[k]+33+j,TestVar.length); | ||
j = j+25; | j = j+25; | ||
} | } | ||
Line 127: | Line 134: | ||
var j = 0; | var j = 0; | ||
for( var k=0; k<oligo2.length; k++ ) { | for( var k=0; k<oligo2.length; k++ ) { | ||
- | TestVar = TestVar.substring(0,index[k]+j) + TestVar.substring(index[k]+j,index[k]+3+j).fontcolor("red") + TestVar.substring(index[k]+3+j,TestVar.length); | + | TestVar = TestVar.substring(0,index[k]+j) + TestVar.substring(index[k]+j,index[k]+3+j).fontcolor("red") + TestVar.substring |
+ | |||
+ | (index[k]+3+j,TestVar.length); | ||
j = j+25; | j = j+25; | ||
} | } | ||
Line 135: | Line 144: | ||
TestVar = TestVar.replace(/</g,"\n <"); | TestVar = TestVar.replace(/</g,"\n <"); | ||
- | + | var w = window.open("blank.html", "blank", "height=50,width=300"); | |
- | + | ||
- | document.writeln("<h2> The inserted sequence is: </h2>"); | + | w.document.writeln("<h2> The inserted sequence is: </h2>"); |
- | document.writeln(TestVar); | + | w.document.writeln(TestVar); |
- | document.writeln("<h1>possible crRNAs are:</h1><div>"); | + | w.document.writeln("<h1>possible crRNAs are:</h1><div>"); |
- | + | w.document.writeln("<table>"); | |
- | document.writeln("<tr><td>"); | + | w.document.writeln("<tr><td>"); |
for (i=0; i<oligo2.length; i++ ) { | for (i=0; i<oligo2.length; i++ ) { | ||
- | 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 " + |
- | document.writeln("<p>Oligo1: " + oligo1[i] + "</p><p>Oligo2: " + oligo2[i] + "</p>"); | + | |
- | document.writeln("<pre>Oligo1: " + oligo1[i] + "<br> ||||||||||||||||||||||||||||||||<br>Oligo2: " + oligo2[i].split("").reverse().join("") + "</pre>"); | + | (parseInt(index[i], 10) + parseInt(1, 10)) + "</h3>"); |
+ | w.document.writeln("<p>Oligo1: " + oligo1[i] + "</p><p>Oligo2: " + oligo2[i] + "</p>"); | ||
+ | w.document.writeln("<pre>Oligo1: " + oligo1[i] + "<br> | ||
+ | |||
+ | ||||||||||||||||||||||||||||||||<br>Oligo2: " + | ||
+ | |||
+ | oligo2[i].split("").reverse().join("") + "</pre>"); | ||
} | } | ||
- | document.writeln("</td>"); | + | w.document.writeln("</td>"); |
- | document.writeln("<td>"); | + | w.document.writeln("<td>"); |
- | document.writeln("</td></tr></table>"); | + | w.document.writeln("</td></tr></table>"); |
- | document.writeln("</div>"); | + | w.document.writeln("</div>"); |
- | document.close(); | + | w.document.close(); |
} | } | ||
</SCRIPT> | </SCRIPT> | ||
+ | <style type="text/css"> | ||
+ | body { | ||
+ | margin:2cm; | ||
+ | font-family: Arial; | ||
+ | color: white; | ||
+ | |||
+ | background-color: #2E2E2E; | ||
+ | } | ||
+ | |||
+ | h1 { | ||
+ | text-align: center; | ||
+ | font-family: Arial; | ||
+ | text-decoration:underline; | ||
+ | } | ||
+ | |||
+ | form { | ||
+ | padding-top:60px; | ||
+ | } | ||
- | <html> | + | textarea { |
+ | width: 40%; | ||
+ | border: 5px solid #999999; | ||
+ | } | ||
+ | |||
+ | fieldset { | ||
+ | width:50%; | ||
+ | float:right; | ||
+ | border: 5px solid #999999; | ||
+ | background-color: #cccccc; | ||
+ | font-family: Arial; | ||
+ | color: black; | ||
+ | } | ||
+ | |||
+ | #h2 { | ||
+ | font-weight: bold; | ||
+ | text-decoration:underline; | ||
+ | } | ||
+ | |||
+ | #explanation { | ||
+ | float:left; | ||
+ | font-family: Arial; | ||
+ | } | ||
+ | |||
+ | |||
+ | |||
+ | </style> | ||
+ | </head> | ||
+ | <body> | ||
+ | <h1>crRNA-Design</h1> | ||
+ | <form action="" method="get"> | ||
+ | <legend>Enter Target Sequence</legend> | ||
+ | <textarea name="Sequenz" type="text" rows="8" cols="40"> | ||
+ | </textarea> | ||
+ | |||
+ | |||
+ | <fieldset> | ||
+ | <p id="h2">Choose Program</p> | ||
+ | <p> | ||
+ | Which strand should be targeted?<br> | ||
+ | <p> | ||
+ | <input type="radio" name="rad" value="1"> non coding strand | ||
+ | <input type="radio" name="rad" value="2"> coding strand | ||
+ | </p> | ||
+ | <p> | ||
+ | <input type="submit" value="submit" name="ok" onClick="CrispR(this.form)" /> | ||
+ | <input type="reset" value="reset"> | ||
+ | </p> | ||
+ | </fieldset> | ||
+ | |||
+ | </form> | ||
+ | <div id="explanation"> | ||
+ | <p>This tool helps you to design a crRNA-insert for pX334a. The oligos contain overhangs which fit to | ||
+ | the BbsI-overhangs by pX334a.</p> | ||
+ | |||
+ | <p>For repression of gene transcription by targeting the coding sequence | ||
+ | it´s crucial to target the non template (= coding) DNA strand. <br> Therefore the oligos must be designed as | ||
+ | follows: | ||
+ | <ol> | ||
+ | <li>Search at your desired target sequence for a CCN (reverse complement of the PAM sequence) at the coding strand.</li> | ||
+ | <li> Extract the following (3') 30 nucleotides.</li> | ||
+ | <li> Extract the reverse complement.</li> | ||
+ | <li>Add AAAC at the 5' end and GT at the 3' end. This will be your fist oligo.</li> | ||
+ | <li>Take the sequence from step 2 and add TAAAAC at the 5' end. This will be your second oligo.</li> | ||
+ | </ol> | ||
+ | </p> | ||
+ | |||
+ | |||
+ | |||
+ | </div> | ||
+ | |||
+ | </body> | ||
+ | </html> |
Revision as of 16:44, 26 September 2013
crRNA-Design
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:
- Search at your desired target sequence for a CCN (reverse complement of the PAM sequence) at the coding strand.
- Extract the following (3') 30 nucleotides.
- Extract the reverse complement.
- Add AAAC at the 5' end and GT at the 3' end. This will be your fist oligo.
- Take the sequence from step 2 and add TAAAAC at the 5' end. This will be your second oligo.