[BioRuby] searching through large sets of features

Michael Barton mail at michaelbarton.me.uk
Fri Apr 10 13:33:30 UTC 2009

There's also some ruby searching algorithms here

I'm happy to try and help if I can



2009/4/10 Michael Barton <mail at michaelbarton.me.uk>

> Would a bloom tree fit this problem?
> http://www.igvita.com/2008/12/27/scalable-datasets-bloom-filters-in-ruby/
> 2009/4/10 Jan Aerts <jan.aerts at gmail.com>
> 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
>> points....)
>> 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?
>> Thanks,
>> jan.
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