[Bioperl-l] Reciprocal best hits using Bioperl?

Jason Stajich jason at bioperl.org
Sun Jan 17 18:59:05 EST 2010


yes - but mcl alone is something slightly different in that it doesn't  
correct for inparalogs, but for incomplete genomes this is probably  
okay.

orthomcl2 does correct the major memory hog problem and efficiencies  
in the parsing in the previous version by relying on the db for the  
indexing and looking of the reciprocal hits.

-jason
On Jan 17, 2010, at 3:12 PM, Tristan Lefebure wrote:

> 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
>>>>> _______________________________________________
>>>>> Bioperl-l mailing list
>>>>> Bioperl-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

--
Jason Stajich
jason.stajich at gmail.com
jason at bioperl.org
http://fungalgenomes.org/



More information about the Bioperl-l mailing list