[Bioperl-l] Any volunteers for doing a Nested Containment List implementation?

Lincoln Stein lstein at cshl.edu
Mon Jul 21 20:02:36 EDT 2008


Hi Folks,

This paper describes an indexing algorithm for genome feature databases
called Nested Containment Lists. Apparently it is substantially faster than
the indexing systems we use in BioPerl for the Bio::DB::GFF,
Bio::DB::SeqFeature::Store, and Chado.

http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btl647v1?papetoc

The concept and data structures are quite simple, and I think it would be
straightforward to implement this system in MySQL tables. Would anybody be
interested in taking this on as a summer project?

Lincoln

-- 
Lincoln D. Stein

Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Stacey Fairfield <Stacey.Fairfield at oicr.on.ca>

Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724 USA
(516) 367-8380
Assistant: Sandra Michelsen <michelse at cshl.edu>


More information about the Bioperl-l mailing list