[Bioclusters] mpiblast

Rodney Dyer rjdyer at vcu.edu
Wed Mar 15 21:50:29 EST 2006

On Wed, 2006-03-15 at 08:17 -0500, Chuming Chen wrote:
> Hi all,
> Does the query size of mpiblast effect the total performance?
> It took about 17 seconds per sequence when I run 721  sequences  (542K) 
> against 22G database.
> But when I run 88532 sequences (47M) against the same database, it  took 
> about 1 minute.
> Can the performance be improved if the query sequence is in a  
> relatively smaller size?
> Thank you for your kind comments and suggestions.
> Chuming Chen
> _______________________________________________
> Bioclusters maillist  -  Bioclusters at bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/bioclusters

On some level, I have to tell my students that we need to place this in
perspective and consider that that you ran 88,532 sequences against a
22G database and it _ONLY_ took you about a minute.  So if you scripted
it, you could possibly get run 42,495,360 sequences in an average work
day and 212,476,800 in an average work week and somewhere in the
neighborhood of 11,048,793,600 for a given year.  Not bad for some small
perl code some data mining.
Rodney J. Dyer, PhD

Department of Biology
Virginia Commonwealth University
Richmond Virginia 23284-2012

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