X-Sieve: cmu-sieve 2.0
Date: Tue, 2 Jul 2002 08:45:06 -0400
Subject: Re: map_db doesn't speed up search
Mime-Version: 1.0 (Apple Message framework v482)
From: "William R. Pearson" <wrp@alpha0.bioch.virginia.edu>
To: Brian Fristensky <frist@cc.UManitoba.CA>
Content-Transfer-Encoding: 7bit
X-DCC-UofM-Metrics: electra 1032; Body=1 Fuz1=1 Fuz2=1


It should only help on the second search - after the data is already in 
memory.  It will not help on the first.

Remember also that, because fasta is slower than blast, the fraction of 
the time spent reading the database is smaller, so the gains are less.   
And it has the biggest effect when lots of searches are done one after 
the other, so that the likelihood of the database staying in memory is 
greater.

There will be a greater improvement for the comp_mlib. version of fasta, 
which compares a library to another library.

Searching the NR database on a 4-processor alpha, I see the elapsed time 
drop from about 45 sec to 41 sec - not very much, but probably a 50% 
improvement in library reading time.


Bill