[BiO BB] Looking for researcher, to assist on blast-like invention

dorje tarap dorjetarap at googlemail.com
Tue Feb 12 09:30:18 EST 2008

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.



On 12/02/2008, Mike Marchywka <marchywka at hotmail.com> 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
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