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Article #2658Re: BLAST software
From: Linlin Yan
Date: Fri, 04 Jul 2008 08:17
Date: Fri, 04 Jul 2008 08:17
24 lines
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3064 bytes
On Jul 3, 12:40�pm, Patrick Flaherty <Patrick_mem...@newsguy.com> wrote: > 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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