Team:Freiburg/Project/modeling/crRNA/js
From 2013.igem.org
(Difference between revisions)
Line 156: | Line 156: | ||
var w = window.open("blank.html", "blank", "height=50,width=300"); | var w = window.open("blank.html", "blank", "height=50,width=300"); | ||
+ | w.document.writeln("<h2> The inserted sequence is: </h2>"); | ||
+ | w.document.writeln(TestVar); | ||
+ | w.document.writeln("<h1>possible crRNAs are:</h1><div>"); | ||
+ | w.document.writeln("<table>"); | ||
+ | w.document.writeln("<tr><td>"); | ||
+ | for (i=0; i<oligo2.length; i++ ) { | ||
+ | |||
+ | 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("<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>"); | ||
+ | |||
+ | } | ||
alert('Working.'); | alert('Working.'); | ||
} | } |
Revision as of 21:55, 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.