Team:NYU/Programming

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.

• Finally got the CGI working - click below or go [http://openwetware.org/images/a/a7/Biobrickprimers.txt here for the source code]

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.

• 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.