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.

Possible workaround: 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 strings.

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.

  • $\begingroup$ Why can't you read in each sequence one at a time, and use regex's to see if the recognition sequences are in there? $\endgroup$ – swbarnes2 Oct 28 '15 at 21:26
  • $\begingroup$ @swbarnes2 I can, but that seems only practical so long as I keep the restrictionbatch small. Vs a real test of hundreds of enzymes is that practical? $\endgroup$ – Atl LED Oct 28 '15 at 21:38
  • $\begingroup$ How long do you think it takes to search for 100 regex sequences in one string? I don't think it will take long. $\endgroup$ – swbarnes2 Oct 28 '15 at 21:41
  • $\begingroup$ @Swbarnes2 that's backing out of using Biopython, but something we're considering. The actual full library we have is about 1200 enzymes, many of which with wildcards. I wanted to make sure something like that didn't already exist before we build it $\endgroup$ – Atl LED Oct 28 '15 at 21:52

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Browse other questions tagged or ask your own question.