Steve et al.,
We'd be curious in hearing about various people's comparisons
of FASTA vs BLAST in terms of sensitivity. We will shortly be
offering both services freely by e-mail from the GenBank On-line
Service. BLAST is fast without a doubt, but does it miss hits more
often than FASTA or is it of comparable sensitivity? I am sure that
one can pull up individual examples which can make either program look
more sensitive, but I'd like to hear the experiences of independent
parties that may have looked into this issue in some detail. I expect
that this question will come up frequently.
kristoff at genbank.bio.net
P.S. - The comparison in the BLAST paper was to FASTP if I recall correctly.