Thank You everyone for the suggestions .. I have decided to use -b 100 option with blastall, and removing -F F option as we currently don't need that. and -v 200 option for formatdb. We are using the NR (non-redundant database from NCBI) as the DB for blast which is currently about 1 GB with ~2.3 Million sequences in it, so what number would be appropriate for "-v" option in formatdb ? Does fragmenting the DB affect the speed of blast computations? -Dina At 10:09 AM 3/10/2005, you wrote: >Dinanath Sulakhe wrote: > > >>Now the Admin of the Site is asking me if its possible to reduce the >>amount of memory these blast jobs use? He says these jobs are requesting >>about 600-700MB of RAM, and he is asking me to reduce it to atmost 500MB. >>Is it possible to reduce the amount of RAM it is requesting by tweaking >>any of the parameters in blast?? > >Yes. Run formatdb similar to this > > formatdb -i $db -o T -p T -v 200 > >where $db is the name of your db as in your blast line below. This will >segment your database down quite a bit. Note: there are limits you would >have to worry about if $db is huge (over 10 GB or so). > >>My blast options are : >>blastall -i $input -o $output -d $db -p blastp -m 8 -F F >>Please let me know, >>Thank you, >>Dina >>_______________________________________________ >>Bioclusters maillist - Bioclusters at bioinformatics.org >>https://bioinformatics.org/mailman/listinfo/bioclusters > >-- >Joseph Landman, Ph.D >Founder and CEO >Scalable Informatics LLC, >email: landman at scalableinformatics.com >web : http://www.scalableinformatics.com >phone: +1 734 786 8423 >fax : +1 734 786 8452 >cell : +1 734 612 4615 > >_______________________________________________ >Bioclusters maillist - Bioclusters at bioinformatics.org >https://bioinformatics.org/mailman/listinfo/bioclusters =============================== Dinanath Sulakhe Mathematics & Computer Science Division Argonne National Laboratory Ph: (630)-252-7856 Fax: (630)-252-5986