[Bioperl-l] HIV db post with linebreaks.

Mark A. Jensen maj at fortinbras.us
Tue Oct 28 14:33:16 EDT 2008


[once more, with linebreaks]
Hello all, 

I've been working on a set of Bioperl modules that access the
(difficult to navigate) Los Alamos HIV sequence database. The modules
have a couple of features that I think could boost the usage of that
resource. What makes LANL really useful is the richness of the
annotations, with information on geography, virology, patient health,
and other epidemiologically useful stuff. However, the db interface is
cgi-based and difficult to use in batch or to create complex queries
without cramping your right index finger. The modules take care of
this, slurp the desired annotations and attach them correctly (I
think) to Bio::Seq objects delivered by a SeqIO stream. The interface
understands NCBI-like query strings (with ANDs, ORs, and parens).
 
I've put the APIs up on my site so as not to cram your inbox: please
see

http://fortinbras.us/HIVQueryAPI 

All the modules exist, work, and have their own .t files. I'd
appreciate your comments.
 
cheers, 
Mark Jensen




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