[Bioperl-l] All-vs-all BLAST

Tony Andreeva tony at mrc-lmb.cam.ac.uk
Tue Jul 20 11:09:29 EDT 2004

To be more precise:

Use bl2seq if you want to compare each two pairs. using bl2seq you will 
avoid formatting

% bl2seq -p blastp -i sequence1 -j sequence2 -o seq1-vs-seq2.out ( and suitable parameters )

Use blastall if you want to search with each sequence against the others

% formatdb -i seq.db -o T
% blastall -p blastp -i seq.db -d seq.db -o seq.out ( and suitable parameters )

By simply typing:

%blastall --help
%bl2seq --help

you can obtain quite detailed help for the program settings.

Hope that helps

Dr.Antonina Andreeva
MRC Centre for Protein Engineering
Hills Road, Cambridge, CB2 2QH
01223 252959 

Peter J Stogios wrote:

> Hello,
> I'm looking for a script to do an all-vs-all BLAST comparison of a set 
> of sequences.  This has been done many times by others and I don't 
> want to "reinvent the wheel", can anyone help me find such a script or 
> utility?
> Thanks,
> ~
> Peter J Stogios
> Grad student, Privé Lab
> Dept. of Medical Biophysics, University of Toronto
> e: pstogios at uhnres.utoronto.ca
> w: http://xtal.uhnres.utoronto.ca/prive
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-
> l

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