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 http://dyerlab.bio.vcu.edu