[Bioclusters] Parallel Sequence Alignment tool

[jgans]

Hello,

There is a nice paper from SGI on parallelizing the Clustal program 
using OpenMP 
(http://www.cs.umd.edu/class/spring2003/cmsc838t/papers2/bio-SGI-parallel-clustal-01.pdf) 
.

Even though this paper refers to an earlier version of Clustal (circa 
2001), it is a very useful guide. Using this paper as a reference, it 
was straight forward to add the required OpenMP code to the most recent 
version of Clustal (I only modified the first stage pairwise alignment 
portion of the code).

Regards,

Jason Gans

Bioscience Division, B-7
Los Alamos National Laboratory



Abhishek Pratap wrote:
> Hey Ognen
>
> Thanks for sharing. Just wondering if you could recommend anything
> good on how to convert single threaded programs into multiones.
> Ofcourse if the base algorithm is compatible. Any good resource that
> you would recommend ?
>
> Thanks,
> -Abhi
>
> On Mon, Aug 24, 2009 at 8:25 AM, Ognen Duzlevski<maketo at sdf.lonestar.org> wrote:
>   
>> On Fri, 17 Jul 2009, slitster at rcn.com wrote:
>>
>>     
>>> Date: Fri, 17 Jul 2009 10:41:53 -0400 (EDT)
>>> From: slitster at rcn.com
>>> Reply-To: HPC in Bioinformatics <bioclusters at bioinformatics.org>
>>> To: bioclusters at bioinformatics.org
>>> Subject: [Bioclusters] Parallel Sequence Alignment tool
>>>
>>> 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.
>>>       
>> I once wrote a multi-threaded version of clustalw - you can get it here:
>> http://naniteworld.com/clustalw_smp-0.99-9.tar.gz
>>
>> Ognen
>>
>> _______________________________________________
>> 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
>
>