[Biodevelopers] Blast not symmetrical?

[Michael Nuhn]

Hi, Marty!

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

One of the genomes I used is unpublished so I can't send you the original
files. However, I could easily reproduce this with two different genomes.

Since this seems to be a complex issue, I summarized it here:
http://nbc3.biologie.uni-kl.de/blast_mystery/

I also put the genomes and blasts there for download.

Perhaps I could also put the solution to this on the page when I know it.

Greetings from Germany,
Michael.

>
> 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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