is there any way you can first use something like BLAST to cut down the search space? i don't really know enough about your application, but trying to find a way to let BLAST do some of the work would be my first instinct. maybe you can get BLAST to give you a list of the substrings with very rough alignments (which it will do very quickly. 10-50k base-pairs is nothing to BLAST) and then just search through those with your regexps.

anders pearson

In reply to Re: Performance Tuning: Searching Long-Sequence Permutations by thraxil
in thread Performance Tuning: Searching Long-Sequence Permutations by Itatsumaki

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