[Bioperl-l] BioXML, Agave and bsml

Lincoln Stein lstein@cshl.org
Wed, 27 Mar 2002 11:46:00 -0500

DAS (what you're calling "BioXML") is well implemented, but is a very shallow 
pipe.  It will transfer the feature table, but not the sequence meta data 
such as author, species, citations, and so on.  You will want to go to the 
www.biodas.org site and get the latest Bio::DAS perl library.

Agave has no support in BioPerl (unless someone has added it very recently).  
BSML is supported and will round-trip BioPerl sequences quite well, but the 
BioPerl parser is a memory hog and rather slow.


On Wednesday 27 March 2002 15:08, Martin Lague wrote:
> I would like to use xml to communicate with my EST database (SQL server). 
> I would
> like to have some advices on wich "protocol" will be the best with BioPerl:
> BioXML (DAS),
> Agave or bsml.  I saw that BioXML seems to be better implemented, but I
> would like to
> know if it's the best protocol to extract data from a database and create a
> sequence
> object in BioPerl or another "protocol" could be better.  I'm ready to
> write a module and
> maybe to release it to the BioPerl community if I'm able to have something
> decent.
> Martin Lague
> Bioinformatician
> Solanum Genomics International Inc.
> P.O. Box 636, Station "A"
> Fredericton, New Brunswick
> E3B 5A6
> email: mlague@fundy.net
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@bioperl.org
> http://bioperl.org/mailman/listinfo/bioperl-l