[Bioclusters] Parallel Sequence Alignment tool

[Kevin M. Carr]

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
**************************


> From: Nick Holway <nick.holway at gmail.com>
> Reply-To: HPC in Bioinformatics <bioclusters at bioinformatics.org>
> Date: Thu, 30 Jul 2009 17:19:13 +0100
> To: HPC in Bioinformatics <bioclusters at bioinformatics.org>
> 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 <bic at genome.chop.edu>:
>> Are you looking to align short reads from ngs, or other data?
>> 
>> ~ juan
>> 
>> On Jul 17, 2009, at 10:41, <slitster at rcn.com> 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  -  Bioclusters at bioinformatics.org
>>> http://www.bioinformatics.org/mailman/listinfo/bioclusters
>>> 
>> 
>> _______________________________________________
>> Bioclusters maillist  -  Bioclusters at bioinformatics.org
>> http://www.bioinformatics.org/mailman/listinfo/bioclusters
>> 
> 
> _______________________________________________
> Bioclusters maillist  -  Bioclusters at bioinformatics.org
> http://www.bioinformatics.org/mailman/listinfo/bioclusters
>