FASTA speed

Roy Smith roy at alanine.phri.nyu.edu
Fri Jan 25 12:47:26 EST 1991

	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
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 at 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!"

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