[Biodevelopers] Blast not symmetrical?

[Martin Gollery]

Hello Michael,

Can you gzip these two and send them to me? I am really curious now...

Marty

On 1/19/07, Michael Nuhn <nuhn at rhrk.uni-kl.de> wrote:
> Hello, Marty!
>
> Thanks for your response:
>
> > This is correct, BLAST is not symmetrical. Some assume that it is and
> > make some pretty serious mistakes.
>
> Which part of the algorithm makes Blast not symmetrical?
>
> > Switch to Smith-Waterman and you
> > will eliminate this problem.
>
> SW of two genomes (2Mb each)? Any programs come to mind that can do that? (I
> really don't know)
>
> 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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