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

aaron.j.mackey at gsk.com aaron.j.mackey at gsk.com
Fri Jul 25 10:59:27 EDT 2008


FYI, there's also (native) support for RTREE-based spatial indices in 
MySQL 5.1 and beyond ...

  http://dev.mysql.com/doc/refman/5.1/en/optimizing-spatial-analysis.html

I once took a day to try to implement this NCL algorithm as a MySQL UDF 
(i.e. written entirely in C), but got bogged down and discouraged.  The 
PostgreSQL implementation is available from the authors, if I remember 
correctly.

-Aaron

bioperl-l-bounces at lists.open-bio.org wrote on 07/21/2008 08:02:36 PM:

> 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>
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