Team:Imperial College London/Software Tool

From 2010.igem.org

(Difference between revisions)
Line 21: Line 21:
   det[5] = "The complement system is part of the innate immune response to an acute infection. Detecting C3 convertase could give medical professionals a rapid method of seeing if a patient is fighting an acute infection.";
   det[5] = "The complement system is part of the innate immune response to an acute infection. Detecting C3 convertase could give medical professionals a rapid method of seeing if a patient is fighting an acute infection.";
   var prefix = "GAATTCGCGGCCGCTTCTAG";
   var prefix = "GAATTCGCGGCCGCTTCTAG";
-
   var promoter = "AATTTTGTCAAAATAATTTTATTGACAACGTCTTATTAACGTTGATATAATTTAAATTTTATTTGAC AAAAATGGGCTCGTGTTGTACAATAAATGT";
+
   var promoter = "AATTTTGTCAAAATAATTTTATTGACAACGTCTTATTAACGTTGATATAATTTAAATTTTATTTGACAAAAATGGGCTCGTGTTGTACAATAAATGT";
   var rbs = "TACTAGAGTCTTCAGAAAGGAGT";
   var rbs = "TACTAGAGTCTTCAGAAAGGAGT";
-
   var scar = "blank";
+
   var scar = "TACTAG";
-
   var cwb = "ATGCGTTCTTATATAAAAGTCCTAACAATGTGTTTTCTGGGGCTCATACTTTTTGTGCCAAC AGCTTTGGCCGATAACTCAGTGAAAAGAGTTGGGGGAAGCAATAGATACGGCACTGCTGTACAAATATCAAAGCAAATGTATTCAA CAGCAAGTACAGCTGTAATTGTTGGTGGGAGTTCCTATGCAGATGCTATTTCAGCAGCACCTCTTGCTTACCAGAAGAATGCGCCA TTGCTTTACACTAATTCTGATAAGCTTTCATATGAAACGAAAACAAGATTGAAAGAGATGCAGACTAAAAATGTAATTATTGTAGG CGGAACACCTGCTGTTTCTTCTAACACTGCTAACCAGATTAAAAGCTTGGGGATAAGTATTAAACGAATTGCAGGAAGCAACCGTT ATGATACGGCTGCACGGGTGGCAAAAGCGATGGGTGCGACTTCAAAAGCTGTTATTTTGAACGGCTTCTTATATGCAGACGCTCCG GCCGTCATCCCTTATGCAGCGAAAAACGGGTATCCAATTCTTTTTACAAATAAAACATCTATAAATAGTGCGACTACGTCTGTGAT AAAAGATAAGGGAATTTCGAGTACCGTTGTTGTAGGAGGCACTGGAAGTATCAGCAATACGGTATACAACAAGTTACCTTCTCCTA CAAGAATTAGCGGTTCAAACAGATATGAGCTTGCTGCAAATATCGTACAAAAACTTAATTTATCAACAAGCACCGTATATGTAAGC AATGGATTCAGCTACCCTGACTCTATTGCAGGAGCTACACTGGCAGCTAAGAAGAAGCAATCTCTTATTCTTACAAATGGTGAAAA TTTATCTACAGGAGCCCGTAAAATTATTGGAAGTAAAAACATGTCAAACTTTATGATTATCGGAAACACTCCTGCCGTAAGCACAA AGGTTGCTAATCAGCTAAAGAATCCAGTTGTA";
+
   var cwb = "ATGCGTTCTTATATAAAAGTCCTAACAATGTGTTTTCTGGGGCTCATACTTTTTGTGCCAACAGCTTTGGCCGATAACTCAGTGAAAAGAGTTGGGGGAAGCAATAGATACGGCACTGCTGTACAAATATCAAAGCAAATGTATTCAACAGCAAGTACAGCTGTAATTGTTGGTGGGAGTTCCTATGCAGATGCTATTTCAGCAGCACCTCTTGCTTACCAGAAGAATGCGCCATTGCTTTACACTAATTCTGATAAGCTTTCATATGAAACGAAAACAAGATTGAAAGAGATGCAGACTAAAAATGTAATTATTGTAGGCGGAACACCTGCTGTTTCTTCTAACACTGCTAACCAGATTAAAAGCTTGGGGATAAGTATTAAACGAATTGCAGGAAGCAACCGTTATGATACGGCTGCACGGGTGGCAAAAGCGATGGGTGCGACTTCAAAAGCTGTTATTTTGAACGGCTTCTTATATGCAGACGCTCCGGCCGTCATCCCTTATGCAGCGAAAAACGGGTATCCAATTCTTTTTACAAATAAAACATCTATAAATAGTGCGACTACGTCTGTGATAAAAGATAAGGGAATTTCGAGTACCGTTGTTGTAGGAGGCACTGGAAGTATCAGCAATACGGTATACAACAAGTTACCTTCTCCTACAAGAATTAGCGGTTCAAACAGATATGAGCTTGCTGCAAATATCGTACAAAAACTTAATTTATCAACAAGCACCGTATATGTAAGCAATGGATTCAGCTACCCTGACTCTATTGCAGGAGCTACACTGGCAGCTAAGAAGAAGCAATCTCTTATTCTTACAAATGGTGAAAATTTATCTACAGGAGCCCGTAAAATTATTGGAAGTAAAAACATGTCAAACTTTATGATTATCGGAAACACTCCTGCCGTAAGCACAAAGGTTGCTAATCAGCTAAAGAATCCAGTTGTA";
-
   var linker = "AGCAGGGGTAGCAGGGCT GGTGGCGGTGGCGGTGGC";
+
   var linker = "AGCAGGGGTAGCAGGGCTGGTGGCGGTGGCGGTGGC";
   var cleavage = new Array();
   var cleavage = new Array();
   cleavage[1] = "AGCTGGCCTCTT";
   cleavage[1] = "AGCTGGCCTCTT";
Line 32: Line 32:
   cleavage[4] = "ATCGACGGACGT";
   cleavage[4] = "ATCGACGGACGT";
   cleavage[5] = "TTATTATCTCGTTCTGAAGAAGAC";
   cleavage[5] = "TTATTATCTCGTTCTGAAGAAGAC";
-
   var aip = "GAAATGCGCCTTAGCAAATTCTTCAGGGACTTCATTCTT CAAAGGAAAAAA";
+
   var aip = "GAAATGCGCCTTAGCAAATTCTTCAGGGACTTCATTCTTCAAAGGAAAAAA";
   var terminator = "TAATAA";
   var terminator = "TAATAA";
   var suffix = "TACTAGTAGCGGCCGCTGCAG";
   var suffix = "TACTAGTAGCGGCCGCTGCAG";
Line 96: Line 96:
|-
|-
|style="width:860px;background:#d5d5d5;border: solid 20px #d5d5d5;" colspan="3"|'''<html>
|style="width:860px;background:#d5d5d5;border: solid 20px #d5d5d5;" colspan="3"|'''<html>
-
<div id="sequenceout"><span id="stem">Awaiting sequence generation... </span><span id="spre" style="color:#F6CF39"></span><span id="spro" style="color:#FC8E42"></span><span id="srbs" style="color:#D34649"></span><span id="ssca" style="color:#ffffff"></span><span id="scwb" style="color:#AB6197"></span><span id="slin" style="color:#6273A8"></span><span id="scle" style="color:#6A9ECD"></span><span id="saip" style="color:#68904E"></span><span id="ster" style="color:#9DB742"></span><span id="ssuf" style="color:#F6CF39"></span></div>
+
<style type="text/css">
 +
#sequenceout {
 +
  width:500px;}
 +
</style>
 +
<div id="sequenceout"><span id="stem">Awaiting sequence generation... </span><span id="spre" style="color:#F6CF39"></span><span id="spro" style="color:#FC8E42"></span><span id="srbs" style="color:#D34649"></span><span id="ssca" style="color:#A851AA"></span><span id="scwb" style="color:#AB6197"></span><span id="slin" style="color:#6273A8"></span><span id="scle" style="color:#6A9ECD"></span><span id="saip" style="color:#68904E"></span><span id="ster" style="color:#9DB742"></span><span id="ssuf" style="color:#F6CF39"></span></div>
</html>'''
</html>'''
|-
|-
Line 106: Line 110:
'''<span style="color:#D34649">Red</span> - Ribosome Binding Site'''
'''<span style="color:#D34649">Red</span> - Ribosome Binding Site'''
-
'''<span style="color:#FFFFFF">White</span> - Scar'''
+
'''<span style="color:#A851AA">Violet</span> - Scar'''
'''<span style="color:#AB6197">Purple</span> - Cell Wall Binding Domain'''
'''<span style="color:#AB6197">Purple</span> - Cell Wall Binding Domain'''

Revision as of 14:13, 20 October 2010

Software Tool
We realised early on that our detection module could be designed with a sensitivity to different proteases. By changing the cleavage site the system can accept a wide variety of inputs. This tool is designed to facilitate a quick custom sequence generation of the entire surface protein construct.
Select Protease Description

This was our primary target. Read our wiki to find out more!
Awaiting sequence generation...

Yellow - Biobrick Prefix/Suffix

Orange - Promoter

Red - Ribosome Binding Site

Violet - Scar

Purple - Cell Wall Binding Domain

Dark Blue - Adjustable Linker

Light Blue - Protease Cleavage Site

Dark Green - Autoinducing Peptide

Light Green - Terminator

Retrieved from "http://2010.igem.org/Team:Imperial_College_London/Software_Tool"