[Bioperl-l] Inquiry on OrthoMCL

Mark A. Jensen maj at fortinbras.us
Mon Jul 26 11:07:35 EDT 2010


Maybe not in the sense of CommandExts, but a BioPerl module that does the "13 
steps" might be very useful. (Not saying anyone should do it :)  )
----- Original Message ----- 
From: "Aaron Mackey" <amackey at virginia.edu>
To: "Mark A. Jensen" <maj at fortinbras.us>
Cc: "BioPerl List" <bioperl-l at bioperl.org>; "Benard Kulohoma" 
<B.Kulohoma at liverpool.ac.uk>
Sent: Monday, July 26, 2010 10:51 AM
Subject: Re: [Bioperl-l] Inquiry on OrthoMCL


> 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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