[BiO BB] Inconsistent Blast Results

[Rob Zimmer]

Please note that Apocom Genomics provides the GrailEXP software which
incorporates BLAST and specific exon, Cpg island ID functions (as well
as many other features).  Anyone interested in learning more, should
e-mail me back.

Robin Zimmer

-----Original Message-----
From: bbb-bounces at bioinformatics.org
[mailto:bbb-bounces at bioinformatics.org] On Behalf Of Rebekah Rogers
Sent: Friday, February 08, 2008 8:57 PM
To: bbb at bioinformatics.org
Subject: [BiO BB] Inconsistent Blast Results

Hi:

I'm currently running blast 2.2.14 locally on my mac.  I've noticed
that the printout from a blastn run at an E cutoff of 10^-10 reads
differently than a blast run at an E cutoff of 10^-7 when hits worse
than 10^-10 are ignored.   Suddenly at 10^-7 new hits with evals of
10^-11 appear that weren't there before and even the relative strength
of different hits can change.

I'm not certain I understand why this is true and it has a huge impact
on my results.  I know that the Eval is dependent on certain constants
taken from the compared sequences, but I don't understand how this
could possibly change when I'm using the exact same input file and
database.

Does anyone have an explanation?

-Rebekah

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