[Bioclusters] Accelerating tblastx jobs

[Ian Korf]

You might want to optimize your BLAST parameters first. What kind of=20
similarities are you looking for? What are your BLAST parameters? Have=20=

you considered BLASTN instead of TBLASTX? What kind of pilot=20
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=20
> tblastx
> jobs and those jobs are quite long. We were wondering if there is a=20
> way to
> "accelerate" each job. Our cluster has 8 dual-processor Athlon MP2200=20=

> nodes,
> each with 2 GB RAM and 120 GB HD. Right now, each of the nodes runs up=20=

> to
> two jobs and everything is under the supervision of SGE. We are=20
> 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=20
> 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
>
> =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
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=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
> 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
> =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
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>
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