Cross Reactor Script

Question

[User 7351]

Hey guys I need a Python script or other script I can reverse engineer to search BLAST to check for primer cross reactivity between species (forward primer, reverse primer, 5k max bp between primer/probe hybridization). Most of these scripts are proprietary. Will anyone help me out with this or brainstorm with me how to design such a script?

Answer 1

[Sean Davis]

Not a direct answer to your question, but I wanted to make sure you were aware of this tool:

http://genome.ucsc.edu/cgi-bin/hgPcr

Access to the source code is available here:

http://genome.ucsc.edu/admin/git.html

[User 7351]

Cool. I am building a new all-in-one tool. I may have to interface with that.