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List:       bioclusters
Subject:    Re: [Bioclusters] Accelerating tblastx jobs
From:       Ian Korf <ik1 () sanger ! ac ! uk>
Date:       2003-07-22 17:09:25
Message-ID: 3F335B8A-BC67-11D7-897F-0003930EC19A () sanger ! ac ! uk
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You might want to optimize your BLAST parameters first. What kind of 
similarities are you looking for? What are your BLAST parameters? Have 
you considered BLASTN instead of TBLASTX? What kind of pilot 
experiments have you performed?

-Ian

On Tuesday, July 22, 2003, at 03:03 PM, Sylvain Foisy wrote:

> Hi,
>
> Our cluster is being use right now by a group that runs a lot of 
> tblastx
> jobs and those jobs are quite long. We were wondering if there is a 
> way to
> "accelerate" each job. Our cluster has 8 dual-processor Athlon MP2200 
> nodes,
> each with 2 GB RAM and 120 GB HD. Right now, each of the nodes runs up 
> to
> two jobs and everything is under the supervision of SGE. We are 
> thinking
> about creating a custom DB created from nt that would held all of nt
> translated with 6 frames and have the users use blastx on this. We 
> would end
> up with 6 times the numner of sequences but we would not be hit by the
> overhead of translating each of the sequence from nt.
>
> Is this making sense?
>
> Sylvain
>
> ===================================================================
> Sylvain Foisy, Ph. D.
> Directeur - operations / Project Manager
> BioneQ - Reseau quebecois de bio-informatique
> U. de Montreal / Genome-Quebec
>
> Adresse postale:
>
> Departement de biochimie
> Pavillon principal
> 2900, boul. Édouard-Montpetit
> Montréal (Québec) H3T 1J4
>
> Tel: (514) 343-6111 x.4066
> Courriel: sylvain.foisy@bioneq.qc.ca
> ===================================================================
>
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