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

Mike Marchywka marchywka at hotmail.com
Tue Feb 12 13:57:06 EST 2008

> I think someone who uses BLAST frequently, and knows it well from a
> user's perspective... might have a better feel for creating a test
> than I might.

It can be hard to solicit problems from people but
it helps if you have some idea a priori what you are trying to accomplish before you test :)
Certainly test what you expect to achieve and see if the tradeoff/"pathological"
cases are what you expect, and then test with pseudo random input
if you have some way to generate an expected result.

To give you an example, right now I'm writing
stuff that re-invents the wheel with a few things I'm ultimately hoping to identify
and improve. I have scripts to generate random numbers to obtain unknown pieces
of genome and "blast" / search against those assuming they will be "negative controls."
Of course, a "hit" would require further examination but you get the idea. On
genome, you get all kinds of "odd stuff" including discovering the unappreciated
but highly conserved sequence "NNNNNNNNNNNNNNNNNNNNNNNNNNNNNN" LOL.
You get the idea.

I also have some splice related code I'm working on and I eventually found out
about particular cases like DSCAM that make good tests. If you are aware of 
hits that normal blast doesn't turn up with typical search parameters, that would
obviously make a good test case.

Most of the papers that came up in the pubmed search probably list open issues
( or else their conclusion would be translated, " therefore, we require not further funding
from our sponsor" LOL) so just reading the literature should give you some relevant ideas.

Also, besides the bio literature, check out computer/algorithm literature at places like citeseer.

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