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

Nigel Brown
Mon, 5 Jan 1998 18:41:57 GMT

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

Bio / DB /           (record and record stream classes)            (record indexing - experimental)
             (database entry class)
           (psi-blast - experimental)               (embl/genbank/ddbj feature table)             (maxhom/hssp multi-alignment)            (read everything)

Bio / Align /         (manipulate multi-alignment)
          (produce html)
          (generate search/alignment)
              (manipulate alignment row)

Bio / Align / Manager /  (Bio::DB::Blastp consumer)   (Bio::DB::Fasta consumer)    (Bio::DB::Hssp consumer) (Bio::DB::PBlastp consumer)   (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:

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

and also inside the Sander group GeneQuiz suite, eg:

Hope this is interesting or useful...


 Nigel P. Brown, Ph.D.                         Tel: +44 (0)1223 494 451  FAX: 468
 European Bioinformatics Institute,   Hinxton,    Cambridge CB10 1SD,   UK
=========== Bioperl Project Mailing List Message Footer =======
Project URL:
To unsubscribe: send email to with message body
unsubscribe vsns-bcd-perl
Please use the account from which you subscribed, or try:
unsubscribe vsns-bcd-perl <old email-address>
To subscribe: send email to with message body
subscribe vsns-bcd-perl
Administrativa: send email to