[Bio-software] Re: BLAST software

Linlin Yan via bio-soft%40net.bio.net (by yanlinlin82 from gmail.com)
Fri Jul 4 03:17:05 EST 2008

On Jul 3, 12:40 pm, Patrick Flaherty <Patrick_mem... from newsguy.com>
> 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

In my opinion, there are differences between BLAST and pure string
matching. String matching do search text literally, without
considering the letter replacing/inserting/deleting probabilities,
which may have significance in biology.

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