[Bioperl-l] Setting Theoretical Database size for bl2seq

Ryan Golhar golharam at umdnj.edu
Wed Oct 26 16:50:37 EDT 2005

Use length of the database: 12,254,801,043.

BLAST will adjust the number to get the effective length...

-----Original Message-----
From: bioperl-l-bounces at portal.open-bio.org
[mailto:bioperl-l-bounces at portal.open-bio.org] On Behalf Of Waibhav
Sent: Wednesday, October 26, 2005 11:13 AM
To: bioperl-l
Subject: [Bioperl-l] Setting Theoretical Database size for bl2seq

Hello List,

This is not a BioPerl question, but I could not find a satisfactory
answer from other sources and would appreciate any help.

I am trying to use bl2seq for comparing query "q" and another genome
"g". Now, for "q" I already have blastall output from an nt database 
containing >2 million
sequences. I understand that to get compatible e values, I need to set 
-d parameter
for bl2seq to the theoretical data size of that nt database. Which 
number from
the following 4 (taken from blastall output) should be used for -d ?

length of database: 12,254,801,043
effective length of database: 12,167,805,299
effective search space: 48671221196
effective search space used: 48671221196

Any pointers/website/docs will be appreciated.

Thank you.


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