[Bioclusters] RE: Bioclusters digest, Vol 1 #108 - 3 msgs

Tue, 27 Aug 2002 11:17:20 -0400

Here is an open source  beowulf BLAST implementation that may be worth =
taking a look at?
http://bioinformatics.fccc.edu/software/OpenSource/beoblast/beoblast.shtm=
l
Cheers
Scott

-----Original Message-----
From: bioclusters-request@bioinformatics.org
[mailto:bioclusters-request@bioinformatics.org]
Sent: Monday, August 26, 2002 12:01 PM
To: bioclusters@bioinformatics.org
Subject: Bioclusters digest, Vol 1 #108 - 3 msgs

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Today's Topics:

   1. Re: Help on BLAST (John Smutko)
   2. Re: Help on BLAST (Mario Belluardo)
   3. RE: Re: Help on BLAST (Wim Glassee)

--__--__--

Message: 1
Date: Sun, 25 Aug 2002 20:19:19 -0400
From: John Smutko <smutt235@attbi.com>
To: bioclusters@bioinformatics.org
Subject: [Bioclusters] Re: Help on BLAST
Reply-To: bioclusters@bioinformatics.org

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 =
=3D
> > > fragments and BLASTing each of those fragments against the =
(entire) =3D
> > > database is super-easy to implement." Could you please tell me how =
to =3D
> > > 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

--__--__--

Message: 2
Date: Mon, 26 Aug 2002 15:03:54 +0200
From: Mario Belluardo <mario.belluardo@ircc.unito.it>
Organization: IRCC
To: bioclusters@bioinformatics.org
Subject: [Bioclusters] Re: Help on BLAST
Reply-To: bioclusters@bioinformatics.org

Hi Sylvain,
I've found and testing seqsplit (and blastunsplit) that you can download
form here

ftp://ftp.cgr.ki.se/pub/prog/MSPcrunch+Blixem/

Here is the web documentation:
http://www.cgr.ki.se/cgr/groups/sonnhammer/MSPcrunch.html

Unfortunately seems it works only with a single-sequence at time, it
means that you cannot submit multi-sequences querys, but you can modify
yourself the source code. I would like to do it, so if you modify it
before me let me know!

Mario

> Message: 2
> Date: Fri, 23 Aug 2002 14:51:14 -0400
> From: Sylvain Foisy <sylvain.foisy@bioneq.qc.ca>
> To: bioclusters@bioinformatics.org
> Subject: [Bioclusters] Re: Help on BLAST
> Reply-To: bioclusters@bioinformatics.org
>=20
> Hi
>=20
> On Friday, August 23, 2002, at 12:01 PM, bioclusters-
> request@bioinformatics.org wrote:
>=20
> > I read your posts saying "splitting the query sequence into small =
=3D
> > fragments and BLASTing each of those fragments against the (entire) =
=3D
> > database is super-easy to implement." Could you please tell me how =
to =3D
> > combine the results, or a link to the solution would be very =
helpful?
>=20
> 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:
>=20
> -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.
>=20
> Any web links that would help us in our quest?
>=20
> Cordially
>=20
> Sylvain
>=20
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> 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
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++

--=20

Dr. Mario Belluardo
Institute for Cancer Research and Treatment
http://www.ircc.it

--__--__--

Message: 3
From: "Wim Glassee" <wim.glassee@ua.ac.be>
To: <bioclusters@bioinformatics.org>
Subject: RE: [Bioclusters] Re: Help on BLAST
Date: Mon, 26 Aug 2002 15:34:04 +0200
Reply-To: bioclusters@bioinformatics.org

Hi,

I had a fast look at the sources for seqsplit and blastunsplit, and
there doesn't seem to be any statistics recalculation of any kind in
there. If you blast smaller pieces of a query sequence against a db, the
statistics will not be the same as for the original blast, so when
merging the output files, you won't end up with the same results. In a
lot of cases even the number of hits and/or hsps will NOT be the same.

Wim

> -----Original Message-----
> From: bioclusters-admin@bioinformatics.org [mailto:bioclusters-
> admin@bioinformatics.org] On Behalf Of Mario Belluardo
> Sent: maandag 26 augustus 2002 15:04
> To: bioclusters@bioinformatics.org
> Subject: [Bioclusters] Re: Help on BLAST
>=20
> Hi Sylvain,
> I've found and testing seqsplit (and blastunsplit) that you can
download
> form here
>=20
> ftp://ftp.cgr.ki.se/pub/prog/MSPcrunch+Blixem/
>=20
> Here is the web documentation:
> http://www.cgr.ki.se/cgr/groups/sonnhammer/MSPcrunch.html
>=20
> Unfortunately seems it works only with a single-sequence at time, it
> means that you cannot submit multi-sequences querys, but you can
modify
> yourself the source code. I would like to do it, so if you modify it
> before me let me know!
>=20
> Mario
>=20
>=20
>=20
> > Message: 2
> > Date: Fri, 23 Aug 2002 14:51:14 -0400
> > From: Sylvain Foisy <sylvain.foisy@bioneq.qc.ca>
> > To: bioclusters@bioinformatics.org
> > Subject: [Bioclusters] Re: Help on BLAST
> > Reply-To: bioclusters@bioinformatics.org
> >
> > 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
=3D
> > > fragments and BLASTing each of those fragments against the
(entire) =3D
> > > database is super-easy to implement." Could you please tell me how
to
> =3D
> > > 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
> > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>=20
>=20
>=20
> --
>=20
> Dr. Mario Belluardo
> Institute for Cancer Research and Treatment
> http://www.ircc.it
> _______________________________________________
> Bioclusters maillist  -  Bioclusters@bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/bioclusters

--__--__--

_______________________________________________
Bioclusters maillist  -  Bioclusters@bioinformatics.org
https://bioinformatics.org/mailman/listinfo/bioclusters

End of Bioclusters Digest