[Bioclusters] Re: Help on BLAST

[Joseph Landman]

Cluster based BLAST has been covered in the recent past (April or May). 
You have several commercial options at this stage.  I do not think there
are active non-commercial efforts in this area outside of individual
lab's work (I would like to know if I am wrong).

Current options if you want to do this today:

(my company nor I have any direct affiliations with these groups)

1) PowerCloud from Blackstone (http://www.blackstonecomputing.com/).  It
will do what you want, albeit returning an XML document that describes
the results rather than the original results.  This is nice for computer
based parsing/presentation.  PowerCloud is a powerful tool, and does far
more than just this.

2) TurboBLAST from TurboGenomics.  They take a different approach, and
also return a modified XML output representing the query.  

(now for the self-serving commercialism, for which I apologize in
advance)

My company is developing this capability.  I have done exactly what you
indicated you would like, twice before (see
http://www.ensoltek.co.kr/tech/BIO/files/SGI-GenomeCluster.pdf , and
http://www.mscsoftware.com/hpc/lifesciences/life.cfm).   I have formed
Scalable Informatics LLC to develop these products (among several other
activities).

(end of commercialism)

Joe

On Fri, 2002-08-23 at 14:51, Sylvain Foisy wrote:
> Hi
> 
> On Friday, August 23, 2002, at 12:01 PM, bioclusters-
> request@bioinformatics.org wrote:
> 
> > I read your posts saying "splitting the query sequence into small =
> > fragments and BLASTing each of those fragments against the (entire) =
> > database is super-easy to implement." Could you please tell me how to =
> > combine the results, or a link to the solution would be very helpful?
> 
> Add me to the list of interested parties to that subject. I would like 
> to know how to write an app that would do these three steps:
> 
> -Splitting a sequence in multiples of, let say, 100 nucleotides;
> -Send each of them to a node for BLASTing;
> -Reassemble the different results into a single report for the users.
> 
> Any web links that would help us in our quest?
> 
> Cordially
> 
> Sylvain
> 
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> Sylvain Foisy, Ph. D.
> Directeur-Operations / Project Manager
> BioNEQ - Le Reseau quebecois de bioinformatique
> Genome-Quebec
> Tel.: (514) 878-9911
> E-mail: sylvain.foisy@bioneq.qc.ca
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> 
> _______________________________________________
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-- 
Joseph Landman, Ph.D
Scalable Informatics LLC
email: landman@scalableinformatics.com
  web: http://scalableinformatics.com
phone: +1 734 612 4615