[Bioclusters] Accelerating tblastx jobs

[Sylvain Foisy]

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 en=
d
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

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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. =C9douard-Montpetit
Montr=E9al (Qu=E9bec) H3T 1J4

Tel: (514) 343-6111 x.4066
Courriel: sylvain.foisy@bioneq.qc.ca
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