[Bioclusters] Re: Help on BLAST

[John Smutko]

Let me state up front that yes, I do work for Blackstone, just sending this
from my home account.  A couple corrections on the Blackstone PowerCloud Blast
info below:
As I believe Joe has stated below, PowerCloud out of the box will split the
database, run the NCBI-BLAST jobs out on the cluster/farm/whatever, and merge
the results into one file with the correct statistics.  The latest versions
support the default pairwise text output as well as tabular output in addition
to XML (-m 0, 7, and 8 args).  Joe is otherwise correct in all his comments.
We have also implemented a version for one customer as a service that splits
the input into the desired number of segments or number of sequences, and this
will be rolled into a future official supported release.   This will allow
splitting of the input, database, or a combination of the two.   My apologies
for the additional commercialism but I just wanted to make sure that the info
that appeared here was correct.

John Smutko
smutt235@attbi.com
"Enjoy yourself, it's later than you think."


>
> Message: 3
> Subject: Re: [Bioclusters] Re: Help on BLAST
> From: Joseph Landman <landman@scalableinformatics.com>
> To: biocluster <bioclusters@bioinformatics.org>
> Cc: biodevelopers <biodevelopers@bioinformatics.org>
> Date: 23 Aug 2002 16:36:31 -0400
> Reply-To: bioclusters@bioinformatics.org
>
> 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
> > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> >
> > _______________________________________________
> > Bioclusters maillist  -  Bioclusters@bioinformatics.org
> > https://bioinformatics.org/mailman/listinfo/bioclusters
> --
> Joseph Landman, Ph.D
> Scalable Informatics LLC
> email: landman@scalableinformatics.com
>   web: http://scalableinformatics.com
> phone: +1 734 612 4615