FASTA speed

Bodo Rak rak at sun1.ruf.uni-freiburg.de
Tue Jan 29 11:59:16 EST 1991

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
>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)
D-7800-Freiburg, FRG

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