[Bioclusters] Memory Usage for Blast - question

Aaron Darling darling at cs.wisc.edu
Wed Mar 9 18:45:41 EST 2005

Dinanath Sulakhe wrote:

> At 05:06 PM 3/9/2005, Lucas Carey wrote:
>> Hi Dina,
>> I don't know how many of the results you actually need. You may free 
>> up some memory by limiting e-value, returned results, and aligned 
>> results.
>> blastall -e 0.0001 -b 25 -v 25
> would limiting the e-value and other parameters reduce the RAM usage??

probably.  blastall processes one query at a time so its memory 
requirements are determined by the largest result size of any one query 
in your data set.  The b/v parameters mentioned by Lucas limit the 
number of results reported for each query, which ought to limit the 
memory consumption of blastall.

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