[Bioperl-l] What does Expect(2) mean in a blast result?

[Steve Chervitz]

The Bioperl blast parser should extract that value and you can obtain
it from an HSP object, via the HSPI::n() method, documented here:

http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/Search/HSP/HSPI.html#POD23

Dave's basically correct in his explanation. It's a result of the
application of sum statistics by the blast algorithm. You can read all
about it in Korf et al's BLAST book. Here's the relevant section:

http://books.google.com/books?id=xvcnhDG9fNUC&pg=PA102&lpg=PA102&dq=blast+sum+statistics&source=web&ots=WIudsJGaCk&sig=v66X3wRLEHvpTLUD36AE5DGpPBY#PPA102,M1

Steve

On Nov 10, 2007 3:04 AM, Dave Messina <David.Messina at sbc.su.se> wrote:
> Hi Amir,
>
> I don't have my BLAST book handy, and my memory is a little fuzzy, but I
> think the Expect(2) you're seeing is the E-value based on both HSPs
> combined. And I think this is why you see the same Expect value for both --
> because it is shared between them (which sounds like what you wanted).
>
> Again, this is just from memory, but I think this is an option that has to
> be turned on rather than something which Blast decides to do on its own.
>
>
> I don't know whether BioPerl reports this or not. Would you mind e-mailing
> me a entire BLAST report as a sample? When I have some time I'd like to play
> around with this a bit.
>
> Thanks,
> Dave
>
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