Team:NYU/Programming

About this Page

• Competent programming skills are quickly becoming a necessity for effectively 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 to produce 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 - go [http://russelldurrett.com/biobrickprimers.html here for an online version! ]

[http://openwetware.org/images/a/a7/Biobrickprimers.txt Biobricking Primers Source]

Overlap Oligo Maker

• Some very fast and efficient DNA assembly methods require parts to overlap in 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://www.russelldurrett.com/overlapoligos.html Check out the new and improved interactive overlap oligo maker.]

[http://openwetware.org/images/6/67/Overlapoligos.txt Overlap Oligos Source]