[Bioperl-l] How to run blastn with -task blastn option from Bio::Tools::Run::StandAloneBlastPlus?

Smithies, Russell Russell.Smithies at agresearch.co.nz
Tue Jun 8 21:28:03 EDT 2010

Have you read the docs?

Do query and subject ($seq1 and $seq2) need to be Bio::Seq objects?


> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Peng Yu
> Sent: Wednesday, 9 June 2010 1:00 p.m.
> To: bioperl-l at lists.open-bio.org
> Subject: [Bioperl-l] How to run blastn with -task blastn option from
> Bio::Tools::Run::StandAloneBlastPlus?
> Hi,
> I need to use Bio::Tools::Run::StandAloneBlastPlus to run the following
> command.
> blastn -task blastn -query first.fa -subject second.fa
> I tried the following code, which works like without the '-task
> blastn' option. Would you please let me know how to supply the option
> in Bio::Tools::Run::StandAloneBlastPlus?
> my $factory = Bio::Tools::Run::StandAloneBlastPlus->new();
>   my $result=$factory->bl2seq(
>     -method=>'blastn',
>     -query=> $seq1,
>     -subject=> $seq2
>   );
>   $factory->cleanup;
> Thank you for you help!
> --
> Regards,
> Peng
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
Attention: The information contained in this message and/or attachments
from AgResearch Limited is intended only for the persons or entities
to which it is addressed and may contain confidential and/or privileged
material. Any review, retransmission, dissemination or other use of, or
taking of any action in reliance upon, this information by persons or
entities other than the intended recipients is prohibited by AgResearch
Limited. If you have received this message in error, please notify the
sender immediately.

More information about the Bioperl-l mailing list