[Bioperl-l] Setting Theoretical Database size for bl2seq
tembe at bioanalysis.org
Wed Oct 26 11:12:37 EDT 2005
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
for bl2seq to the theoretical data size of that nt database. Which
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.
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