An excellent idea. I would add to it by suggesting that you implement a parser for the resulting BLAST report. The BLAST algorithm extends a maximal scoring segment and will pick up substrings that do not perhaps meet minimum length requirements etc. This is where the parser comes in. Set up bioperl (www.bioperl.org) on your system and use Bio::SearchIO for parsing your report for relevant hits.

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

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