roy at alanine.phri.nyu.edu (Roy Smith) writes:
>I've often seen comments on these newsgroups, like the one from
>rak at sun1.ruf.uni-freiburg.de (Bodo Rak) today, to the effect that they can
>run FASTA against the whole GenBank database on a PC in 20 minutes.
>Frankly, these numbers astound me; I didn't think PCs were anywhere near
>This brings up the question, however, of what kind of PC are we
>talking about? I'm used to things like 10 Mhz 286 machines (I do all my
- staff deleted -
Below I will try to give a more precise estimate of the performance of
Fasta on a quite ordinary AT-type PC uder realistic conditions:
I have tested the speed of a 20MHz 386 PC by scanning the entire EMBL
data base (release 24, 37,784 entries comprising 47,354,438 nt) against a
750 nt long test sequence (ktup=6) with the following results:
Scan time: 36'50''; total CPU time including the top 50 alignments: 38'16''.
A 20MHz 386 machine is certainly nothing fancy nowadays. Many of the
laptops are already equipped with this processor. I hope that the above data
encourage those not having acccess to more efficient computers not to
underestimate the capability of their PCs (or should I say of Fasta even
on a PC?).
The PC which I used in the test is equipped with a co-processor. I don't
think, however, that Fasta makes much use of it.
Department of Biology III (Genetics)
RAK at SUN1.RUF.UNI-FREIBURG.DBP.DE