Re: Parallel Sequence Alignment tool

Nick,

Have you checked out this resource:

http://rdp.cme.msu.edu/

(Note, while I work at MSU I am not affiliated with the Ribosomal Database
Project.)

They have a fully developed pipeline for classifying 16s rRNA sequences.
You can create your own account to processes sequences through their
pipeline.
 =

Kevin M. Carr

**************************
Bioinformatics Specialist
Research Technology
  Support Facility
S20-A Plant Biology Lab
Michigan State University
East Lansing, MI  48824

Ph: (517) 355-6759 x102
Fax:(517) 355-6758
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> From: Nick Holway <[email protected]>
> Reply-To: HPC in Bioinformatics <[email protected]>
> Date: Thu, 30 Jul 2009 17:19:13 +0100
> To: HPC in Bioinformatics <[email protected]>
> Subject: Re: [Bioclusters] Parallel Sequence Alignment tool
> =

> Hello,
> =

> Steve actually posted this on behalf of me, so to cut out the middle
> man I'll answer.
> =

> I'm trying to assist a scientist with a bioinformatics project. He's
> trying to align 16s rDNA sequences to identify the bacterial species.
> I launched a Muscle job on his behalf which took ~5.5 days to run (on
> 3GHz "Harpertown" Xeons). The file the scientist gave me had ~5000
> sequences in which were mostly 1000-1500 bases long.
> =

> I'm trying to persuade the scientist to see if he can reduce the
> number of sequences that he needs to align and also to see if his data
> needs to let Muscle run to completion rather than just the first two
> iterations.
> =

> My reason for wanting to know if there are any good parallel sequence
> alignment tools is that we've seen some excellent speed increases with
> our MD code. Knowing this scientist I imagine he'll need the entire
> data set to be aligned :)
> =

> If you need me to find out any more information from the scientist
> please let me know.
> =

> Thanks
> =

> Nick
> =

> 2009/7/22 Juan Carlos Perin <[email protected]>:
>> Are you looking to align short reads from ngs, or other data?
>> =

>> ~ juan
>> =

>> On Jul 17, 2009, at 10:41, <[email protected]> wrote:
>> =

>>> Does anyone have recommnedations for a parallel sequence alignment tool
>>> =

>>> User investigation so far has turned up clustalW-MPI, but it seams to be
>>> using an older version of clustalW.
>>> =

>>> Any imput much appreciated.
>>> =

>>> Cheers
>>> =

>>> Steve
>>> =

>>> _______________________________________________
>>> Bioclusters maillist =A0- [email protected]
>>> http://www.bioinformatics.org/mailman/listinfo/bioclusters
>>> =

>> =

>> _______________________________________________
>> Bioclusters maillist =A0- [email protected]
>> http://www.bioinformatics.org/mailman/listinfo/bioclusters
>> =

> =

> _______________________________________________
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