If I specify the search space via -dbsize flag among blasts of the same query to multiple databases, the e-values will be comparable among all the results because the search space will be consistent.
Can I assume that will be the same for different blast programs? If I specify the same -dbsize for blastp, blastx, tblastn on different databases, will the result e-values also be comparable? Will search space be calculated differently for a blastx/tblastn/tblastx where 6 frame translations are done?
Let me give an example case. Let's say I want to blast my nucleotide query to a set of 100 protein sequences and a set of 50 nucleotide sequences. I want to use blastx for the 100 protein sequences and tblastx for the 50 nucleotide sequences. My database is really 150 sequences, but I have to split them into 2 due to protein/nucleotide content.
So if I set -dbsize for both blastx and tblastx as 150, would I get comparable e-values?
What if I did blastp and blastn?