roy@alanine.phri.nyu.edu (Roy Smith) (01/26/91)
I've often seen comments on these newsgroups, like the one from
rak@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
that fast.
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
real work on Suns and Macs and just use PC's to control bits of lab
equipment and act as bootservers for bits of network gear). Should I expect
to get search times like that on those sorts of machines, or at the people
who claim these speeds using 30-MHz 386's with multi-Mbytes of RAM; an
entirely different sort of beast?
--
Roy Smith, Public Health Research Institute
455 First Avenue, New York, NY 10016
roy@alanine.phri.nyu.edu -OR- {att,cmcl2,rutgers,hombre}!phri!roy
"Arcane? Did you say arcane? It wouldn't be Unix if it wasn't arcane!"rak@sun1.ruf.uni-freiburg.de (Bodo Rak) (01/30/91)
roy@alanine.phri.nyu.edu (Roy Smith) writes: >I've often seen comments on these newsgroups, like the one from >rak@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 >that fast. >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. Bodo Rak Department of Biology III (Genetics) University D-7800-Freiburg, FRG RAK@SUN1.RUF.UNI-FREIBURG.DBP.DE