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

[Amir Karger]

Thanks for the reply. I'm curious as to how BLAST decides to do this,
but not curious enough to buy the BLAST book.

If you want to see this, you could just tblastn the ENSP00000349467
sequence vs. the genome:
 
MADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADG
NGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDE
EVDEMIREADIDGDGQVNYEEFVQMMTAK
against the human genome at NCBI or locally.
 
I've attached the tblastn report for that protein, which includes the
results I quoted. (It was done as part of a blast of 150 proteins vs.
the genome.)
 
-Amir


________________________________

	From: dave at davemessina.com [mailto:dave at davemessina.com] On
Behalf Of Dave Messina
	Sent: Saturday, November 10, 2007 6:04 AM
	To: Amir Karger
	Cc: bioperl-l
	Subject: Re: [Bioperl-l] What does Expect(2) mean in a blast
result?
	
	
	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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