[Bio-software] Re: BLAST software

[Linlin Yan]

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