[Bioclusters] Memory Usage for Blast - question

Dinanath Sulakhe sulakhe at mcs.anl.gov
Thu Mar 10 13:48:14 EST 2005

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?


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,
>>Bioclusters maillist  -  Bioclusters at bioinformatics.org
>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

Dinanath Sulakhe
Mathematics & Computer Science Division
Argonne National Laboratory
Ph: (630)-252-7856      Fax: (630)-252-5986

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