[Bioclusters] Parallel Sequence Alignment tool
Ognen Duzlevski
maketo at SDF.LONESTAR.ORG
Thu Aug 27 15:04:26 EDT 2009
It would have been nice to be aware of this paper when I parallelized
ClustalW back in 2001/2. The program is not that complicated to
parallelize - it is your basic search for what takes up most time and how
much that portion lends itself to being parallelized. I don't remember
that well - it has been a while - but if I remember correctly ClustalW had
three phases - 1st one was sequence-to-sequence alignment which was very
easy to parallelize, the second phase was irrelevant time-wise to consider
and the third one was where significant time was spent but it was more
difficult to parallelize...
Regards,
Ognen
On Tue, 25 Aug 2009, jgans wrote:
> Date: Tue, 25 Aug 2009 09:04:35 -0600
> From: jgans <jgans at lanl.gov>
> Reply-To: HPC in Bioinformatics <bioclusters at bioinformatics.org>
> To: HPC in Bioinformatics <bioclusters at bioinformatics.org>
> Subject: Re: [Bioclusters] Parallel Sequence Alignment tool
>
> 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
>>
>>
>
> _______________________________________________
> Bioclusters maillist - Bioclusters at bioinformatics.org
> http://www.bioinformatics.org/mailman/listinfo/bioclusters
>
--
Ognen Duzlevski
Independent IT consultant
(561)452-5653
U.S.A.
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