OligoSelect

OligoSelect is a program written in Python that can be used to create oligos for microarrays. This script batch processes genes/ORFS and finds oligos of a length determined by the user. It can be used to find oligos for many genes/ORFs at once. It checks to make sure they are of the specified GC content, that they are unique in the genome database of interest, and that they are not self-annealing. It looks at the region towards the 5' end, preferentially choosing oligos that match the criteria that are closer to the 5' end.

To use this script

1. The user must be able to run it on a machine that can do batch blast queries. These tools can be downloaded from NCBI.
2. The user must load the database they need to have the oligos blasted against
3. Python version 2.1 or later is required

Source Code

Source code tarred and gzipped

oligoselect.tar.gz

If you use this program or would like to add to the code, please contact tracytcaltech.edu, so you can be updated on new releases and bug fixes. Also, the code is under CVS, so contact me if you would like access to the CVS repository.

Documentation