[Bioperl-l] Setting Theoretical Database size for bl2seq

Waibhav Tembe tembe at bioanalysis.org
Wed Oct 26 11:12:37 EDT 2005

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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