[Bioperl-l] Easily parsable command line BLAST output

Jason Stajich jason at bioperl.org
Fri Oct 2 12:41:42 EDT 2009

Depends on what information you want to parse out.... do you need the  
actual alignment?  If no -> use -m 8 or -m 9 and you will have a  
tabular output that is easy to parse even without bioperl.

On Oct 2, 2009, at 9:29 AM, Ben Busby wrote:

> Pardon the simple question, as I am new-ish to Perl, Bioperl, and
> Computational Biology..
> I am doing a whole bunch of large BLAST searches and am wondering  
> what the
> best command line BLAST commands are to put the output in a format  
> best
> parsable by Bio::SearchIO.
> Thanks!
> Ben
> -- 
> Economically, nothing is ever "extended by popular demand".
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Jason Stajich
jason.stajich at gmail.com
jason at bioperl.org

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