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[Bio-software] BLAST software

Patrick Flaherty via bio-soft%40net.bio.net (by Patrick_member from newsguy.com)
Wed Jul 2 23:40:19 EST 2008


Hi - experienced programmer curious about bioinformatics.

The BLAST software package seems to figure in prominently.  Have looked it up
and read some about it (and I'm already familiar with most of the biology that
gets mentioned in the context of BLAST).

Is it fair to say(hopefully not a gross oversimplification) that the BLAST
software might be construed, in some sense, as string matching?

If so, then I would assume that algorithms that speed up string matching might
also speed up BLAST?  I'm sure a great many researchers and bioinformaticians
have looked at this issue a great deal (speeding up BLAST - although the
trade-off seems to be the exactness of the matches), but I've had my own
experience in looking at/using/experimenting with many different approaches to
string matching.

thanx - pat



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