[Bioperl-l] Bio::SearchIO::megablast

Jason Stajich jason at bioperl.org
Thu May 29 12:37:32 EDT 2008


Please ask questions on the mailing list.
There is a link to speed issues in Bio::SearchIO on the wiki.

Depending on what you are doing, you can dump out data as tabular  
format when you run BLAST.
-jason
Begin forwarded message:

> From: "Thomas Nussbaumer" <praktikant at h-net.com>
> Date: May 29, 2008 3:11:14 AM CDT
> To: <jason at bioperl.org>
> Subject: Bio::SearchIO::megablast
>
> hi,
> is there any possibility to
>
> a)
> improve the performance, make search faster,
> currently i am using a .txt file which contains the hsp
> under XP
>
> b)
> have to used this module with more than ~1000000
> how long did it take to parse the file
>
> best regards
> Thomas



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