Team:NYU/Programming

From 2010.igem.org

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* This script allows the user to input a DNA sequence and outputs the primers necessary for biobricking that sequence via PCR. The script calculates Tm but does not (yet) consider primer dimers.  
* This script allows the user to input a DNA sequence and outputs the primers necessary for biobricking that sequence via PCR. The script calculates Tm but does not (yet) consider primer dimers.  
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*Finally got the CGI working - go [http://russelldurrett.com/biobrickprimers.html here for an online version! ]
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*Finally got the CGI working - click below or go [http://openwetware.org/images/a/a7/Biobrickprimers.txt here for the source code]
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[http://openwetware.org/images/a/a7/Biobrickprimers.txt Biobricking Primers Source]
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<html>
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<a href="http://russelldurrett.com/biobrickprimers.html"><img src="http://2010.igem.org/wiki/images/7/77/Biobricking_Primers_Logo.gif"/></a>
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</html>
=====Overlap Oligo Maker=====
=====Overlap Oligo Maker=====
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* Some very fast and efficient DNA assembly methods require parts to overlap on the ends of their sequences. This script will take two DNA sequences and output the oligos (and their Tms) one would need to PCR constructs with overlapping ends.  
* Some very fast and efficient DNA assembly methods require parts to overlap on the ends of their sequences. This script will take two DNA sequences and output the oligos (and their Tms) one would need to PCR constructs with overlapping ends.  
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*I'm a CGI machine! [http://www.russelldurrett.com/overlapoligos.html Check out the new and improved interactive overlap oligo maker.]
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*I'm a CGI machine! [http://openwetware.org/images/6/67/Overlapoligos.txt Here is the source code.] or click below for an interactive version.
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[http://openwetware.org/images/6/67/Overlapoligos.txt Overlap Oligos Source]
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<html>
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<a href="http://www.russelldurrett.com/overlapoligos.html"><img src="http://2010.igem.org/wiki/images/7/74/Overlap_Oligos_Logo.gif" width="300" height="200" /></a></html>

Revision as of 06:59, 25 October 2010




About this Page
  • Competent programming skills are quickly becoming a necessity for working in biology. Because most of our team members had never had exposure to a programming environment, we decided to use the obstacles presented in our iGEM experiments as cause for learning the Perl programming language and produced some simple scripts that could do routine iGEM labors for us. Here are some examples:
Biobricking Primers
  • This script allows the user to input a DNA sequence and outputs the primers necessary for biobricking that sequence via PCR. The script calculates Tm but does not (yet) consider primer dimers.

Overlap Oligo Maker
  • Some very fast and efficient DNA assembly methods require parts to overlap on the ends of their sequences. This script will take two DNA sequences and output the oligos (and their Tms) one would need to PCR constructs with overlapping ends.