the bioinformatics chat

This time you’ll hear from Fabio Cunial on the topic of Markov models and space-efficient data structures. First we recall what a Markov model is and why variable-order Markov models are an improvement over the standard, fixed-order models. Next we discuss the various data structures and indexes that allowed Fabio and his collaborators to represent these models in a very small space while still keeping the queries efficient. Burrows-Wheeler transform, suffix trees and arrays, tries and suffix link trees, and more!

Links:

• The preprint: A framework for space-efficient variable-order Markov models
• The book: Genome-Scale Algorithm Design
• The GitHub repo

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