[Bioperl-l] a query-based interface to the LANL HIV db

Mark A. Jensen - Fortinbras Research jensen at fortinbras.us
Tue Oct 28 11:31:55 EDT 2008


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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