[Bioperl-l] Fwd: megablast using bioperl

Smithies, Russell Russell.Smithies at agresearch.co.nz
Mon Feb 1 16:02:12 EST 2010

Sorry, I missed the megablast bit.
There's a Bio::SearchIO module for reading megablast output but I don't think there's any built-in way of executing it.
You may have to use system() to execute the command then read the output back into Bio::SearchIO

Have you had a look at Blastplus?


From: Xiujing Gu [mailto:xiujingg at yahoo.com]
Sent: Tuesday, 2 February 2010 9:39 a.m.
To: 'BioPerl List'; Smithies, Russell
Subject: RE: [Bioperl-l] Fwd: megablast using bioperl

Thanks for the links!
But, they only talk about the regular blastall program, not the megablast.

I am not sure how can I switch from blastall to megablast. I tried to just call megablast, but I got a very differenct report.

$VAR1 = bless( {
                 'primary_seq' => bless( {
                                           'display_id' => 'test',
                                           '_seq_length' => undef,
                                           '_root_verbose' => 0,
                                           'alphabet' => 'dna'
                                         }, 'Bio::PrimarySeq' ),
                 '_root_verbose' => 0
               }, 'Bio::Seq' );
Can't locate object method "nextSbjct" via package "Bio::Seq"

Xiujing Gu

--- On Mon, 2/1/10, Smithies, Russell <Russell.Smithies at agresearch.co.nz> wrote:

From: Smithies, Russell <Russell.Smithies at agresearch.co.nz>
Subject: RE: [Bioperl-l] Fwd: megablast using bioperl
To: "'BioPerl List'" <bioperl-l at lists.open-bio.org>
Cc: "'xiujingg at yahoo.com'" <xiujingg at yahoo.com>
Date: Monday, February 1, 2010, 3:12 PM
Have you read the docs? It's very well documented:

Have you searched the BioPerl wiki? Again, well documented with examples:

And if that doesn't help, perhaps you need to improve your Google skills:


> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org</mc/compose?to=bioperl-l-bounces at lists.open-bio.org> [mailto:bioperl-l-
> bounces at lists.open-bio.org</mc/compose?to=bounces at lists.open-bio.org>] On Behalf Of Jason Stajich
> Sent: Tuesday, 2 February 2010 8:48 a.m.
> To: BioPerl List
> Cc: xiujingg at yahoo.com</mc/compose?to=xiujingg at yahoo.com>
> Subject: [Bioperl-l] Fwd: megablast using bioperl
> Xiujing -
> Your message is best asked on the mailing list.
> Begin forwarded message:
> > From: Xiujing Gu <xiujingg at yahoo.com</mc/compose?to=xiujingg at yahoo.com>>
> > Date: February 1, 2010 7:58:55 AM PST
> > To: jason at bioperl.org</mc/compose?to=jason at bioperl.org>
> > Subject: megablast using bioperl
> >
> > Hello Jason:
> >
> > After numerous googling, I found you might be the only person who
> > knows about this subject. Would you so kindly show me an example of
> > setting up megablast using bioperl Bio::Tools::Run::StandAloneBlast?
> >
> > Thanks a lot!
> >
> > Best regards,
> > Xiujing
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org</mc/compose?to=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