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...)
 
(2 intermediate revisions not shown)
Line 95: Line 95:
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;
Line 102: Line 108:
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 == "") {
Line 109: Line 115:
} 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
Line 116: Line 122:
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;
 +
}
}
Line 125: Line 135:
<form name="RBSinput" action="" method="get">
<form name="RBSinput" action="" method="get">
Enter RBS DNA sequence:<br>
Enter RBS DNA sequence:<br>
-
<input type="text" name="RBSdna" size=40 value=""> example: TCACACAGGAAACC<br><br>
+
<input type="text" name="RBSdna" size=40 value=""> example: TCACACAGGAAACC<br>
 +
or select a BioBrick RBS:<br>
-
RBS RNA sequence:<br>
+
<select name="BioBrickSelect" onChange="document.RBSinput.RBSdna.value=document.RBSinput.BioBrickSelect.options[document.RBSinput.BioBrickSelect.selectedIndex].value">
-
<input type="text" name="RBS" size=40 value="" readonly="readonly"> example: UCACACAGGAAACC<br><br>
+
<option value=TTCACACAGGAAACC>BBa_B0029 - 1 bp deletion from B0031</option>
 +
<option value=AUUAAAGAGGAGAAA>BBa_B0030 - RBS.1 (strong) -- modified from R. Weiss</option>
 +
<option value=UCACACAGGAAACC>BBa_B0031 - RBS.2 (weak) -- derivative of BBa_0030</option>
 +
<option value=UCACACAGGAAAG>BBa_B0032 - RBS.3 (medium) -- derivative of BBa_0030</option>
 +
<option value=UCACACAGGAC>BBa_B0033 - RBS.4 (weaker) -- derivative of BBa_0030</option>
 +
<option value=AAAGAGGAGAAA>BBa_B0034 - RBS (Elowitz 1999) -- defines RBS efficiency</option>
 +
<option value=ATTAAAGAGGAGAA>BBa_B0035  - RBS (B0030 derivative)</option>
 +
<option value=AAAGAGGGGAAA>BBa_B0064 - Tuned RBS for Q04401</option>
 +
<option value=TCACACCACCC>BBa_B0074 - Orthogonal RBS</option>
 +
<option value=UUUCUCCUCUUUAAU>BBa_J44001 - Reverse RBS (RBSrev) -- corresponds to BBa_B0030</option>
 +
<option value=AAAGAGGGGACA>BBa_J61100 - Ribosome Binding Site Family Member</option>
 +
<option value=AAAGACAGGACC>BBa_J61101 - Ribosome Binding Site Family Member</option>
 +
<option value=AAAGAUCCGAUG>BBa_J61102 - Ribosome Binding Site Family Member</option>
 +
<option value=AAAGAUUAGACA>BBa_J61103 - Ribosome Binding Site Family Member</option>
 +
<option value=AAAGAAGGGACA>BBa_J61104 - Ribosome Binding Site Family Member</option>
 +
<option value=AAAGACAUGACG>BBa_J61105 - Ribosome Binding Site Family Member</option>
 +
<option value=AAAGAUAGGAGA>BBa_J61106 - Ribosome Binding Site Family Member</option>
 +
<option value=AAAGAAGAGACU>BBa_J61107 - Ribosome Binding Site Family Member</option>
 +
<option value=AAAGACGAGAUA>BBa_J61108 - Ribosome Binding Site Family Member</option>
 +
<option value=AAAGACUGGAGA>BBa_J61109 - Ribosome Binding Site Family Member</option>
 +
<option value=AAAGAGGCGAAU>BBa_J61110 - Ribosome Binding Site Family Member</option>
 +
<option value=AAAGAGGCGAUA>BBa_J61111 - Ribosome Binding Site Family Member</option>
 +
<option value=AAAGAGGUGACA>BBa_J61112 - Ribosome Binding Site Family Member</option>
 +
<option value=AAAGAGUGGAAA>BBa_J61113 - Ribosome Binding Site Family Member</option>
 +
<option value=AAAGAUGAGAAG>BBa_J61114 - Ribosome Binding Site Family Member</option>
 +
<option value=AAAGAAGGGAUA>BBa_J61115 - Ribosome Binding Site Family Member</option>
 +
<option value=AAAGACAUGAGG>BBa_J61116 - Ribosome Binding Site Family Member</option>
 +
<option value=AAAGACAUGAGU>BBa_J61117 - Ribosome Binding Site Family Member</option>
 +
<option value=AAAGAGACGAAU>BBa_J61118 - Ribosome Binding Site Family Member</option>
 +
<option value=AAAGAUUUGAUA>BBa_J61119 - Ribosome Binding Site Family Member</option>
 +
<option value=AAAGACGCGAGA>BBa_J61120 - Ribosome Binding Site Family Member</option>
 +
<option value=AAAGAGACGAGU>BBa_J61121 - Ribosome Binding Site Family Member</option>
 +
<option value=AAAGAGAGGAGC>BBa_J61122 - Ribosome Binding Site Family Member</option>
 +
<option value=AAAGAGAUGACU>BBa_J61123 - Ribosome Binding Site Family Member</option>
 +
<option value=AAAGAGCCGACA>BBa_J61124 - Ribosome Binding Site Family Member</option>
 +
<option value=AAAGAGCCGAGU>BBa_J61125 - Ribosome Binding Site Family Member</option>
 +
<option value=AAAGAGGUGACU>BBa_J61126 - Ribosome Binding Site Family Member</option>
 +
<option value=AAAGAGUGGAAC>BBa_J61127 - Ribosome Binding Site Family Member</option>
 +
<option value=AAAGAUAGGACU>BBa_J61128 - Ribosome Binding Site Family Member</option>
 +
<option value=AAAGAUUGGACG>BBa_J61129 - Ribosome Binding Site Family Member</option>
 +
<option value=AAAGAAACGACA>BBa_J61130 - Ribosome Binding Site Family Member</option>
 +
<option value=AAAGAACCGAAU>BBa_J61131 - Ribosome Binding Site Family Member</option>
 +
<option value=AAAGACAGGAUU>BBa_J61132 - Ribosome Binding Site Family Member</option>
 +
<option value=AAAGACCCGAGA>BBa_J61133 - Ribosome Binding Site Family Member</option>
 +
<option value=AAAGACCGGAAA>BBa_J61134 - Ribosome Binding Site Family Member</option>
 +
<option value=AAAGACCGGAGA>BBa_J61135 - Ribosome Binding Site Family Member</option>
 +
<option value=AAAGAGCUGAGC>BBa_J61136 - Ribosome Binding Site Family Member</option>
 +
<option value=AAAGAGUAGAUC>BBa_J61137 - Ribosome Binding Site Family Member</option>
 +
<option value=AAAGAUAUGAAU>BBa_J61138 - Ribosome Binding Site Family Member</option>
 +
<option value=AAAGAUUAGAGU>BBa_J61139 - Ribosome Binding Site Family Member</option>
 +
<option value=CCCGCCGCCACCAUGGAG>BBa_J63003 - designed yeast Kozak sequence</option>
 +
<option value=AUUAAAGAGGAGAAAUA>BBa_K082000 - reconstruct strong RBS</option>
 +
<option value=UCACACAGGAAAGUA>BBa_K082001 - RBS medium</option>
 +
<option value=AAAGAGGAGAAAUA>BBa_K082002 - RBS defines RBS efficiency</option>
 +
<option value=CCCGCCGCCACCAUGGAG>BBa_K165002 - Kozak sequence (yeast RBS)</option>
 +
</select>
 +
 
 +
<br><br>
<!--<input type="submit" value="Generate Key and Lock" />-->
<!--<input type="submit" value="Generate Key and Lock" />-->
Line 134: Line 202:
<br><br>
<br><br>
-
<hr><br>
+
RBS RNA sequence:<br>
 +
<input type="text" name="RBS" size=40 value="" readonly="readonly"> example: UCACACAGGAAACC<br><br>
-
<b>Key stuff:</b><p>
 
-
Upstream<br>
 
-
<input type="text" name="KEYupsteam" value="ACCCAAAGUCC" readonly="readonly" size=40><p>
 
-
Downstream<br>
 
-
<input type="text" name="KEYdownsteam" value="UGGUUAAUGAAAAUUAACUUA" readonly="readonly" size=40><p>
 
-
Further Downstream (optional part)<br>
 
-
<input type="text" name="KEYfurtherdownsteam" value="AAAAAGCCGAGUUAUUAAUCCGGCUU" readonly="readonly" size=40>
 
-
<br><br>
 
-
<hr><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>
-
<b>Lock stuff:</b><p>
 
-
Upstream<br>
 
-
<input type="text" name="LOCKupsteam" value="UUUGGGUAGAUCAC" readonly="readonly" size=40><p>
 
-
Scar + Start Codon<br>
 
-
<input type="text" name="LOCKscar" value="UACUAGAUG" readonly="readonly" size=40><p>
 
-
Mismatch sequence<br>
 
-
<input type="text" name="LOCKmismatch" value="GGAC" readonly="readonly" size=40><p>
 
-
Scar complement<br>
 
-
<input type="text" name="LOCKscarcomp" value="GUA" readonly="readonly" size=40><p>
 
-
Position (bp) of mismatch in the reverse complment of RBS<br>
 
-
<input type="text" name="LOCKposmis" value="3" readonly="readonly" size=40>
 
-
<br><br>
 
<hr><br>
<hr><br>
Key RNA sequence:<br>
Key RNA sequence:<br>
Line 178: Line 231:
<textarea rows="5" cols="80" name="genlockDNA" wrap="soft">
<textarea rows="5" cols="80" name="genlockDNA" wrap="soft">
</textarea>
</textarea>
-
<p>
+
<br><br>
 +
<hr><br>
 +
 +
<b>Key variables:</b><p>
 +
Upstream<br>
 +
<input type="text" name="KEYupsteam" value="ACCCAAAGUCC" readonly="readonly" size=40><p>
 +
Downstream<br>
 +
<input type="text" name="KEYdownsteam" value="UGGUUAAUGAAAAUUAACUUA" readonly="readonly" size=40><p>
 +
Further Downstream (optional part)<br>
 +
<input type="text" name="KEYfurtherdownsteam" value="AAAAAGCCGAGUUAUUAAUCCGGCUU" readonly="readonly" size=40>
 +
<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>
 +
 +
<b>Lock variables:</b><p>
 +
Upstream<br>
 +
<input type="text" name="LOCKupsteam" value="UUUGGGUAGAUCAC" readonly="readonly" size=40><p>
 +
Scar + Start Codon<br>
 +
<input type="text" name="LOCKscar" value="UACUAGAUG" readonly="readonly" size=40><p>
 +
Mismatch sequence<br>
 +
<input type="text" name="LOCKmismatch" value="GGAC" readonly="readonly" size=40><p>
 +
Scar complement<br>
 +
<input type="text" name="LOCKscarcomp" value="GUA" readonly="readonly" size=40><p>
 +
Position (bp) of mismatch in the reverse complment of RBS<br>
 +
<input type="text" name="LOCKposmis" value="3" readonly="readonly" size=40>
 +
<br><br>
</form>
</form>

Latest revision as of 10:10, 8 August 2009

Ribo Key & Lock Generator

Enter RBS DNA sequence:
example: TCACACAGGAAACC
or select a BioBrick RBS:




RBS RNA sequence:
example: UCACACAGGAAACC

Key RBS reverse complement RNA sequence with two mismatches:


Lock RBS reverse complement RNA sequence with one mismatch:



Key RNA sequence:

Lock RNA sequence:

Jump to mfold


Key DNA sequence:

Lock DNA sequence:



Key variables:

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 variables:

Upstream

Scar + Start Codon

Mismatch sequence

Scar complement

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


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