[Bioperl-l] mpiblast

Heikki Lehvaslaiho heikki.lehvaslaiho at gmail.com
Sat Sep 18 03:41:22 EDT 2010


Been running 1.6 and its betas on Blue Gene/P for months. The output
is identical to standard BLAST output. No issues in parsing it with
BioPerl.

     -Heikki

Heikki Lehvaslaiho - skype:heikki_lehvaslaiho
cell: +966 545 595 849  office: +966 2 808 2429

Computational Bioscience Research Centre (CBRC), Building #2, Office #4216
4700 King Abdullah University of Science and Technology (KAUST)
Thuwal 23955-6900, Kingdom of Saudi Arabia




On 16 September 2010 21:25, Dave Messina <David.Messina at sbc.su.se> wrote:
>> Is the there a standalone like module that allows you to easily call mpiblast?
>
> No, although with Mark Jensen's new WrapperBase system, writing one would probably be pretty straightforward.
>
>        http://www.bioperl.org/wiki/Module:Bio::Tools::Run::WrapperBase
>
>
>> I'm assuming seqio with parse a mpiblast output file correctly?
>
> Yes, although I see that a new version of mpiblast was recently released.
>
> Has anyone out there tested BioPerl against mpiBLAST 1.6.0 output yet?
>
>
> Dave
>
>
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