Steven Smith <ssmith at itis.com> writes:
> You do need to be careful when comparing e-values. They take into account
> the size of the database searched. The e-value means "I expect to find X
> hits when searching this sequence with a database of size Y." So e-values
> are comparable when Y's match.
Although "bit" scores are not so intuitive, Steve Smith's post
highlights their advantage over E()-values. Both blast2 and fasta33
"bit" scores attempt to summarize the same information, which is
database size and query size independent.