BLAST results (was RE: [Biodevelopers] Blast not symmetrical?)

[Angulo, David]

Marty (or anyone),

Perhaps you can explain this to me.  I searched an AA string against the rat genome.  I got a poor hit (e-value about 50), so I decided to see if there was a homologous gene, and I searched against all genomes.  Instead of returning the same hit (or better), but best hit I received was about 360!  Why is this?  I'm confounded.

Thanks for your help.

Dave


-----Original Message-----
From: biodevelopers-bounces+dangulo=cti.depaul.edu at bioinformatics.org on behalf of Martin Gollery
Sent: Wed 1/17/2007 5:23 PM
To: Development in Bioinformatics
Subject: Re: [Biodevelopers] Blast not symmetrical?
 
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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