Counting, generating and sampling tree alignments
Julien Courtiel

14 January 2016, 11:00 - 14 January 2016, 12:00 Salle/Bat : 465/PCRI-N
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Activités de recherche : Structural biology

Résumé :

Pairwise ordered tree alignment are combinatorial objects that appear in important applications, such as RNA secondary structure comparison. However, the usual representation of tree alignments is ambiguous, which is detrimental to any probabilistic analysis.

In this talk, we see how to remove this ambiguity. We give for that a context-free grammar that generates every tree alignment exactly once. Then two applications are presented. The first one is a precise asymptotic enumeration of tree alignments, obtained by mean of basic analytic combinatorics. The second application is an efficient dynamic programming algorithm for sampling alignments under the Gibbs-Boltzmann probability distribution.