[BioRuby] searching through large sets of features

Jan Aerts jan.aerts at gmail.com
Fri Apr 10 07:30:32 UTC 2009

Hi all,
I need to be able to handle millions of features for a visualization and
therefore be able to search through them efficiently. I've been made aware
of a so-called R-Tree (http://en.wikipedia.org/wiki/R-tree) data structure
that could do just that. One of the issues that this approach would solve is
that it doesn't need to load every single feature when the display
resolution is not high enough (no use trying to plot 5 million points next
to each other on a screen of 800 pixels wide; you can only plot 800

I'm now trying to write a ruby-implementation of an R-Tree that is more fit
for loci (i.e. one less dimension than an R-Tree, and has to handle
chromosome as well) at http://github.com/jandot/locustree. I'm trying to
make it a module that can be mixed in, so anything which has a chromosome,
start and stop can be indexed and searched using this R-Tree adaptation.

Does anyone know a ruby-implementation of R-Tree? Or is anyone interested in
helping me out?


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