[Bioperl-l] limit the number of blast output per query

Ross KK Leung ross at cuhk.edu.hk
Thu Jul 7 02:43:10 UTC 2011

I know this question should submit to BLAST help but it seems they have
already been overwhelmed by incoming emails. I wonder any bioperl users
happen to know how to limit the number of blast output per query. For
example, for human genome as a database to blast against, a single query can
generate 10,000+ hits. I have already supplied -b 30 -v 30 flags but
obviously the blastall from blast2.2.22 does not "obey" my instruction. 

The output files generated are usually larger than 100G+ but indeed the
final ones that I want usually are only of 10M-. Is there any way to help
save our Earth (Not exaggerated, energy is WASTED in a meaningless manner)?

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