Team:TUDelft/RiboKeyLock Generator

From 2009.igem.org

(Difference between revisions)
(New page: {{Template:TUDelftiGEM2009}} =Ribo Key & Lock Generator= <html> <script type="text/javascript"> <!-- // TUDelft iGEM 2009 // Generate Ribo Keys and Locks for a specific RBS // Version 0...)
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Kdownsteam = document.RBSinput.KEYdownsteam.value;
Kdownsteam = document.RBSinput.KEYdownsteam.value;
Kfardownsteam = document.RBSinput.KEYfurtherdownsteam.value;
Kfardownsteam = document.RBSinput.KEYfurtherdownsteam.value;
-
+
        KEYposmis1 = document.RBSinput.KEYposmis1.value;
 +
        KEYposmis2 = document.RBSinput.KEYposmis2.value;
 +
KrevcomRBSmis1 = insertmismatch(revcomp(RBS),KEYposmis1);
 +
        KrevcomRBSmis2 = insertmismatch(KrevcomRBSmis1,KEYposmis2);
 +
 
 +
 
 +
 
Lupstream = document.RBSinput.LOCKupsteam.value;
Lupstream = document.RBSinput.LOCKupsteam.value;
Lscar = document.RBSinput.LOCKscar.value;
Lscar = document.RBSinput.LOCKscar.value;
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Lposmis = document.RBSinput.LOCKposmis.value;
Lposmis = document.RBSinput.LOCKposmis.value;
-
revcomRBSmis = insertmismatch(revcomp(RBS),Lposmis);
+
LrevcomRBSmis = insertmismatch(revcomp(RBS),Lposmis);
if (document.RBSinput.RBS.value == "") {
if (document.RBSinput.RBS.value == "") {
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} else {
} else {
//RNA
//RNA
-
document.RBSinput.genkey.value = Kupsteam + RBS + Kdownsteam + revcomp(RBS) + Kfardownsteam;
+
document.RBSinput.genkey.value = Kupsteam + RBS + Kdownsteam + KrevcomRBSmis2 + Kfardownsteam;
-
document.RBSinput.genlock.value = Lscarcomp + revcomRBSmis + Lmismatch + Lupstream + RBS + Lscar;
+
document.RBSinput.genlock.value = Lscarcomp + LrevcomRBSmis + Lmismatch + Lupstream + RBS + Lscar;
//DNA
//DNA
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document.RBSinput.genlockDNA.value = rnatodna(document.RBSinput.genlock.value);
document.RBSinput.genlockDNA.value = rnatodna(document.RBSinput.genlock.value);
 +
                //show mismatches
 +
                document.RBSinput.KEYrevcommisRBS.value = KrevcomRBSmis2;
 +
                document.RBSinput.LOCKrevcommisRBS.value = LrevcomRBSmis;
 +
}
}
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<a href="#" onclick="calckeylock()" title=""><img src="https://static.igem.org/mediawiki/2009/7/7a/TUD-ribo-keylock-button.png" border="0"></a>
<a href="#" onclick="calckeylock()" title=""><img src="https://static.igem.org/mediawiki/2009/7/7a/TUD-ribo-keylock-button.png" border="0"></a>
<br><br>
<br><br>
 +
 +
Key RBS reverse complement RNA sequence with two mismatches:<br>
 +
<input type="text" name="KEYrevcommisRBS" size=40 value="" readonly="readonly"><br><br>
 +
 +
Lock RBS reverse complement RNA sequence with one mismatch:<br>
 +
<input type="text" name="LOCKrevcommisRBS" size=40 value="" readonly="readonly"><br><br>
<hr><br>
<hr><br>
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<input type="text" name="KEYfurtherdownsteam" value="AAAAAGCCGAGUUAUUAAUCCGGCUU" readonly="readonly" size=40>
<input type="text" name="KEYfurtherdownsteam" value="AAAAAGCCGAGUUAUUAAUCCGGCUU" readonly="readonly" size=40>
<br><br>
<br><br>
-
 
+
Position 1 (bp) of mismatch in the reverse complment of RBS<br>
 +
<input type="text" name="KEYposmis1" value="8" readonly="readonly" size=40>
 +
<br><br>
 +
Position 2 (bp) of mismatch in the reverse complment of RBS<br>
 +
<input type="text" name="KEYposmis2" value="9" readonly="readonly" size=40>
 +
<br><br>
<hr><br>
<hr><br>

Revision as of 08:07, 5 August 2009

Ribo Key & Lock Generator

Enter RBS DNA sequence:
example: TCACACAGGAAACC

RBS RNA sequence:
example: UCACACAGGAAACC



Key RBS reverse complement RNA sequence with two mismatches:


Lock RBS reverse complement RNA sequence with one mismatch:



Key stuff:

Upstream

Downstream

Further Downstream (optional part)


Position 1 (bp) of mismatch in the reverse complment of RBS


Position 2 (bp) of mismatch in the reverse complment of RBS



Lock stuff:

Upstream

Scar + Start Codon

Mismatch sequence

Scar complement

Position (bp) of mismatch in the reverse complment of RBS



Key RNA sequence:

Lock RNA sequence:

Jump to mfold


Key DNA sequence:

Lock DNA sequence:

Retrieved from "http://2009.igem.org/Team:TUDelft/RiboKeyLock_Generator"