[Bioperl-l] Blasting 100kb against dbEST?

Chris Fields cjfields at illinois.edu
Wed May 6 16:49:46 EDT 2009

I have locally run ~100kb fragments before (BLASTN) w/o problems off  
my first-gen MacBook, but this was against a small database.  If you  
need to iterate through the sequence in chunks you can specify start/ 
stop with -L, so the hits/HSPs will be mapped accordingly (instead of  
starting from 1).

Also, mpiBLAST appears to segment queries:



On May 6, 2009, at 2:37 PM, Scott Cain wrote:

> Hi all,
> I'm working on a project that needs to BLAST 100kb genomic fragments
> against large DBs like dbEST.  Now, 100kb is a big query, and I was
> hoping that there might be a standard way to break this apart,
> parallelize the BLAST and then reassembly/collate the results.  Is
> there a standard way to do that?  That is, the first two things are
> easy to do, but putting it all back together seems fraught with traps.
> Its those traps I'm looking for.
> Thanks,
> Scott
> -- 
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at  
> scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
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