Hi Mike, "Faster than blast" or even "more accurate than blast" type algorithms have been around for some time now. Some interesting examples are patternhunter (commercial) http://www.bioinformaticssolutions.com/products/ph/ and YAST (opensource); Both claim to be significantly faster and more accurate than BLAST, unfortunately they are not as popular.
I suspect this is for a few reasons: Blast has been around for a while, and has gained some confidence in the bioinformatics sector; The reporting of the statistical significance (e-values) is easy to interpret; And it has a large genomics database readily available. For an algorithm to replace blast, it would have to tick a lot of these boxes. Your approach seems pretty interesting as you mention it is not a heuristic algorithm, whereas the main approach recently seems to be using the "spaced-seeds" concept introduced in PatternHunter. Your approach sounds somewhat similar to the four-russians speedup and any way to speed up the dynamic programming algorithm, without sacrificing speed would benefit a number of feilds, not just bioinformatics. I guess, the first step would be to outline your algorithm into a draft paper to get a better understanding of your approach. HTH Karma On 12/02/2008, Mike Marchywka <[EMAIL PROTECTED]> wrote: > > > > >> I also use many tricks to reuse computations across various proteins. > >> For example, the matrix for protein "ABCDE", is identical, at first > > Have you gotten any blast source code? This would be a good thing to > start with for a number of reasons. But, don't assume that a given > implementation > is either well optimized of naive. Sure, they could have > code like > > get_parameters(); > metric=do_expensive_metric_thing(); > if ( metric > _________________________________________________________________ > Helping your favorite cause is as easy as instant messaging. You IM, we > give. > http://im.live.com/Messenger/IM/Home/?source=text_hotmail_join > _______________________________________________ > BBB mailing list > [email protected] > http://www.bioinformatics.org/mailman/listinfo/bbb > _______________________________________________ BBB mailing list [email protected] http://www.bioinformatics.org/mailman/listinfo/bbb
