I have a collection of about 120 7kB sequences I would like to check for ether a list of specific restriction sites, or what restriction sites might be absent in all of them.
Is there a app or library that can do this?
So far I've only found systems that can do 1 or 2 sequences at a time.
Right now I'm trying to concatenate all the sequences together (about 850Mb) and then using Bio.Restrictions methods of the Biopython libraries. As I kept running into memory overflow problems, I'm refining the search make a new
RestrictionBatch based on 4-5 enzymes that are absent and introduce-able into 3-4 test sequences.
Even then I'm running into crashes, which will probably mean that I take the complete set and test over five or so combined
Before I completely go re-inventing the wheel, can anyone let me know of something that already does this? I don't really care about the language, we have Python, .Net, Java, R, and MatLab "covered" across the lab.