Bioperl: send me pointers/links/code for your favorite Blast module !

[Nigel Brown]

I've written some classes that take searches (blast,fasta,etc) or
alignments and squirt out pretty HTML.

The underlying parsers all subclass from a kind of incremental parser based
around, possibly nested, records. Search output (blast,fasta) and flatfile
databases (EMBL,Genbank) exist. None is complete, and I just add a new
subclass for parsing particular (sub)records as the need arises. There's
also some elementary provision for a kind of hierarchical indexing. The
original goal was to have some kind of meta-description for each parser
(pattern/action?) that would be used to generate perl code on-the-fly using
the boilerplate methods in Bio::DB::Record, but I never had time and never
will now!

I haven't written the pod yet, unfortunately, but here's a rough class
layout:

Bio / DB / Record.pm           (record and record stream classes)
	   Index.pm            (record indexing - experimental)
           Entry.pm            (database entry class)
           Blastp.pm 
	   Blastx.pm 
	   Fasta.pm 
	   PBlastp.pm          (psi-blast - experimental)
	   Embl.pm 
	   Genbank.pm
	   FT.pm               (embl/genbank/ddbj feature table)
	   Hssp.pm             (maxhom/hssp multi-alignment)
	   Slurp.pm            (read everything)

Bio / Align / Align.pm         (manipulate multi-alignment)
      	      Display.pm       (produce html)
      	      Manager.pm       (generate search/alignment)
      	      Row.pm           (manipulate alignment row)

Bio / Align / Manager / Blastp.pm  (Bio::DB::Blastp consumer)
    			Fasta.pm   (Bio::DB::Fasta consumer)
    			Hssp.pm    (Bio::DB::Hssp consumer)
    			PBlastp.pm (Bio::DB::PBlastp consumer)
    			Plain.pm   (Bio::DB::Slurp consumer)


The consumers, eg., Bio::Align::Manager::Blastp::scan_entry() and then
Bio::Align::Manager::Blastp::parser(), give some idea of how to use the
underlying parsers.


You can check out the code and preliminary documentation if you wish:

    http://www.sander.ebi.ac.uk/mview/

MView is also running inside the EBI fasta/blast web service:

    http://www2.ebi.ac.uk/blast2/ or http://www2.ebi.ac.uk/fasta3/

and also inside the Sander group GeneQuiz suite, eg:

    http://www.sander.ebi.ac.uk/gqsrv/submit


Hope this is interesting or useful...

Thanks
nigel

-- 
---------------------------------------------------------------------------
 Nigel P. Brown, Ph.D.                               Nigel.Brown@ebi.ac.uk 
 http://www.sander.ebi.ac.uk/~brown/    Tel: +44 (0)1223 494 451  FAX: 468
 European Bioinformatics Institute,   Hinxton,    Cambridge CB10 1SD,   UK
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