[Biodevelopers] RE: Biodevelopers Digest, Vol 22, Issue 4

[Thompson, William]

Hi

The e-value is the number of different alignments with scores equivalent
to or better than the score S, that are expected to occur in a database
search by chance. The lower the E value, the more significant the score.
The particular e-value depends on the size of the database. When you
searched against all genomes, you increased the size of the database and
the score you received from the sequence rat database was no longer
significant. Originally, you expected to get 50 hits that good by chance
in a random database the size of the rat genome. When you search all of
the genomes, even your best hit would be expected to have 360 scores
that good in a random database the size of all the genomes. The hit you
originally got in the rat database was probably beyond the e-value
cutoff for your search.

Bill



-----Original Message-----


Message: 4
Date: Thu, 18 Jan 2007 16:30:17 -0600
From: "Angulo, David" <dangulo at cti.depaul.edu>
Subject: BLAST results (was RE: [Biodevelopers] Blast not
	symmetrical?)
To: <mgollery at unr.edu>,	"Development in Bioinformatics"
	<biodevelopers at bioinformatics.org>
Message-ID:
	<6BE417C96732934A83E4BBBB3B7FF2F4046471B3 at haydn.cti.depaul.edu>
Content-Type: text/plain; charset="iso-8859-1"

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