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BFs are getting pretty popular in bioinformatics. The post mentions one example, here is my favorite recent one: http://minia.genouest.org/files/minia.pdf http
by roye 13y ago
BFs are getting pretty popular in bioinformatics. The post mentions one example, here is my favorite recent one: http://minia.genouest.org/files/minia.pdf http://minia.genouest.org/files/minia.pdf
- sakai 13y agoVery cool – I hadn't seen this paper before (haven't done any real work on de novo assembly or otherwise requiring de Bruijn graphs). Here's a paper using Bloom filters in metagenomic classification (my relative* area): http://bioinformatics.oxfordjournals.org/content/26/13/1595.long http://bioinformatics.oxfordjournals.org/content/26/13/1595.... In this vein, a friend and I are researching/implementing a probabilistic key-value store for some bioinformatics applications (one is metagenomic organism and gene identification). It's fast and space-efficient, just like a BF (though obviously less so as it stores keys and not single-set-membership). Any use cases for that kind of thing in your sub-field? Always trying to figure out interesting new applications (we aren't ready to write it all up yet, but hope to at some point not too far down the road). * I'm really just a dabbler / don't have a formal bioinformatics background. My friend is the genetics PhD.
- roye 13y agoCan you explain "probabilistic key-value store?" Would it be that each gene has some defined probability of belonging to a given organism, or is it probabilistic in the sense of having a defined error rate as BFs do?
- sakai 13y agoThe latter - probabilistic in the sense of having a defined error rate. In one of our use cases, the keys are simply kmers and the values are organism or gene IDs.