[Biodevelopers] Blast not symmetrical?

[Martin Gollery]

This is correct, BLAST is not symmetrical. Some assume that it is and
make some pretty serious mistakes. Switch to Smith-Waterman and you
will eliminate this problem.

Marty

On 1/17/07, Michael Nuhn <nuhn at rhrk.uni-kl.de> wrote:
> Hello, Everybody!
>
> While I was trying to track down a "bug" in my program I found out that the
> blast program (Blastn v2.2.11) is not symmetrical, that is:
>
> If I blast a query sequence Q against a database S (1 sequence), I get a
> result set B(S,Q).
>
> If I do the blast the other way around, that is, I use S as query sequence
> and blast it against the database Q, I get a result B(Q,S).
>
> And the problem is: B(S,Q) and B(Q,S) are not equal. Each blast set has some
> blast hits that the other does not have and also some blast hits that have
> one common coordinate but end at another.
>
> Both blasts were made with the blast defaults, no filter was used. The two
> sequences are large (~2Mb each, the sequences are genomes). According to the
> statistics used in blast (at least the part I understand), it should not
> play a role which sequence is the query and which is the subject.
>
> Does anyone have an explanation for this? Since I don't really have a clue
> at where to start, hints and wild guesses are also appreciated.
>
> Thanks in advance,
> Michael.
>
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-- 
-- 
Martin Gollery
Associate Director
Center For Bioinformatics
University of Nevada at Reno
Dept. of Biochemistry / MS334
775-784-7042
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