David Jones <David.Jones at brunel.ac.uk> writes:
>> Although I'm not going to argue with what Bill says here - it might be
> worth noting that the above comment applies to "normal" Blast only.
I agree. While statistical estimates for single sequence searches have
become very reliable over the past 4 years or so, estimates for
profile searches are more problematice, particularly when the
statistical parameters are pre-calculated from simulations of
The need to use much more conservative thresholds for profile-type
searches effectively reduces the sensitivity of the method.