[Bioperl-l] Reciprocal best hits using Bioperl?

Tristan Lefebure tristan.lefebure at gmail.com
Sun Jan 17 18:12:56 EST 2010


The transition to orthoMCL v2 being a bit painful (you need 
a MySQL database), I recently switched directly to MCL and 
the accompanying mclblastline and co programs. Modular, 
simple and very fast. Following some simulations, It gives 
better results with incomplete genomes than orthoMCL v1.x 
...

http://micans.org/mcl/

--Tristan

On Sunday 17 January 2010 17:00:02 Chris Fields wrote:
> OrthoMCL has updated to v2 and no longer uses BioPerl,
>  just plain perl.  Database is available here:
> 
> http://orthomcl.org/cgi-bin/OrthoMclWeb.cgi
> 
> Package (you'll need a few other things to get it
>  working):
> 
> http://orthomcl.org/common/downloads/software/
> 
> chris
> 
> On Jan 17, 2010, at 3:10 PM, Bhakti Dwivedi wrote:
> > Thank you!
> >
> > On Sun, Jan 17, 2010 at 4:03 PM, Mark A. Jensen 
<maj at fortinbras.us> wrote:
> >> re Chris's answer, check out this archived post:
> >> http://bioperl.org/pipermail/bioperl-l/2008-March/0273
> >>57.html cheers MAJ
> >> ----- Original Message ----- From: "Bhakti Dwivedi" <
> >> bhakti.dwivedi at gmail.com>
> >> To: <bioperl-l at lists.open-bio.org>
> >> Sent: Sunday, January 17, 2010 11:02 AM
> >> Subject: [Bioperl-l] Reciprocal best hits using
> >> Bioperl?
> >>
> >>
> >> Hi
> >>
> >>> Is there a Bio-perl module to parse the reciprocal
> >>> best hits (query1-> hit1
> >>> && hit1 -> query1)  from a blast table report?
> >>>
> >>> Thanks
> >>>
> >>> BD
> >>> _______________________________________________
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> >
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