[Bioclusters] Re: Help on BLAST

[Wim Glassee]

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