Re: Parallel Sequence Alignment tool

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 <[email protected]>
> Reply-To: HPC in Bioinformatics <[email protected]>
> To: HPC in Bioinformatics <[email protected]>
> 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<[email protected]> 
>> wrote:
>> 
>>> On Fri, 17 Jul 2009, [email protected] wrote:
>>>
>>> 
>>>> Date: Fri, 17 Jul 2009 10:41:53 -0400 (EDT)
>>>> From: [email protected]
>>>> Reply-To: HPC in Bioinformatics <[email protected]>
>>>> To: [email protected]
>>>> 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  -  [email protected]
>>> http://www.bioinformatics.org/mailman/listinfo/bioclusters
>>>
>>> 
>> 
>> _______________________________________________
>> Bioclusters maillist  -  [email protected]
>> http://www.bioinformatics.org/mailman/listinfo/bioclusters
>>
>> 
>
> _______________________________________________
> Bioclusters maillist  -  [email protected]
> http://www.bioinformatics.org/mailman/listinfo/bioclusters
>

--
Ognen Duzlevski
Independent IT consultant
(561)452-5653
U.S.A.
--