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Old 07-02-2010, 09:50 AM   #5
sjmillerAZ
Junior Member
 
Location: Tucson, AZ

Join Date: Oct 2008
Posts: 3
Default blast+ vs older blastall

I've seen the same behavior for blast+ vs the older blastall. In section 4.5 of the NCBI user manual for blast+ they show a performance improvement over blastall for queries of length 10Kb - 10Mb, but for shorter queries my experience is that blast+ is much, much slower. When I run a blastx with 50 DNA queries of average length 1135 against a protein database of 475000 sequences (161M total letters) using 8 cpus, the blastall 2.2.18 code finishes the run in just under 5 hours with cpu usage 764%. The same blastx with blast+ version 2.2.23 is still running after 16 hours and has only finished 14000 queries, and the cpu usage shows 243% for 8 processors. Needless to say, I won't be encouraging anyone with shorter queries to use blast+ until this problem has been fixed.
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