[Bioclusters] Re: Help on BLAST

[Mario Belluardo]

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