[Bioperl-l] Inquiry on OrthoMCL

Chris Fields cjfields at illinois.edu
Mon Jul 26 11:05:05 EDT 2010


Agreed; I'm using it locally.  I could see subclassing BLAST (or similar) wrappers specifically for the all-v-all portion of the pipeline (for consistency/flexibility), but I get along w/o that.

chris

On Jul 26, 2010, at 9:51 AM, Aaron Mackey wrote:

> OrthoMCL is more of a pipeline than a standalone tool; I'm not sure it makes
> sense to "wrap" it.
> 
> See: http://orthomcl.org/common/downloads/software/v2.0/UserGuide.txt
> 
> -Aaron
> 
> On Mon, Jul 26, 2010 at 9:18 AM, Mark A. Jensen <maj at fortinbras.us> wrote:
> 
>> Hi Benard,
>> Forwarding to the list for more help for you. You may want to look at the
>> POD for Bio::Tools::Run::WrapperBase::CommandExts (in the bioperl-live
>> distribution) in the section "DEVELOPER INTERFACE" for a tutorial on how to
>> use this module to create an OrthoMCL wrapper. This might be more technical
>> than you want. Maybe a dev on the list would be interested in creating a
>> wrapper using CommandExts.
>> cheers, MAJ
>> ----- Original Message ----- From: "Benard Kulohoma" <
>> B.Kulohoma at liverpool.ac.uk>
>> To: <maj at fortinbras.us>
>> Sent: Wednesday, July 21, 2010 10:58 AM
>> Subject: Inquiry
>> 
>> 
>> Hi Mark,
>> 
>> I just read your bioperl resource on BWA (and here:
>> http://bioperl.org/pipermail/bioperl-l/2009-July/030563.html) and it was
>> most helpful. Do you have any idea of how I could use Bioperl to implement
>> OrthoMCL of several bacterial genomes. I would like to find some membrane
>> proteins.
>> 
>> Many thanks,
>> 
>> Benard
>> 
>> PS: I am sorry for spaming/inquiring!! :)
>> 
>> --
>> The Wellcome Trust Sanger Institute is operated by Genome Research
>> Limited, a charity registered in England with number 1021457 and a
>> company registered in England with number 2742969, whose registered
>> office is 215 Euston Road, London, NW1 2BE.
>> 
>> 
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