[Bioclusters] Parallel Sequence Alignment tool

Nick Holway nick.holway at gmail.com
Thu Jul 30 12:19:13 EDT 2009


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

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.



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

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