Counting, generating and sampling tree alignments

Cedric Chauve 1 Julien Courtiel 1 Yann Ponty 2, 3
3 AMIB - Algorithms and Models for Integrative Biology
LIX - Laboratoire d'informatique de l'École polytechnique [Palaiseau], LRI - Laboratoire de Recherche en Informatique, UP11 - Université Paris-Sud - Paris 11, Inria Saclay - Ile de France, Polytechnique - X, CNRS - Centre National de la Recherche Scientifique : UMR8623
Abstract : 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 as supertrees is ambiguous, i.e. two distinct supertrees may induce identical sets of matches between identical pairs of trees. This ambiguity is uninforma-tive, and detrimental to any probabilistic analysis. In this work, we consider tree alignments up to equivalence. Our first result is a precise asymptotic enumeration of tree alignments, obtained from a context-free grammar by mean of basic analytic combinatorics. Our second result focuses on alignments between two given ordered trees S and T. By refining our grammar to align specific trees, we obtain a decomposition scheme for the space of alignments, and use it to design an efficient dynamic programming algorithm for sampling alignments under the Gibbs-Boltzmann probability distribution. This generalizes existing tree alignment algorithms, and opens the door for a probabilistic analysis of the space of suboptimal alignments.
Type de document :
Communication dans un congrès
ALCOB - 3rd International Conference on Algorithms for Computational Biology - 2016, Jun 2016, Trujillo, Spain. 2016, 〈http://grammars.grlmc.com/AlCoB2016/〉
Liste complète des métadonnées

https://hal.inria.fr/hal-01154030
Contributeur : Yann Ponty <>
Soumis le : samedi 12 décembre 2015 - 10:53:28
Dernière modification le : mardi 8 mars 2016 - 01:06:08
Document(s) archivé(s) le : samedi 29 avril 2017 - 11:44:23

Fichiers

CombinatoricsTreeAlignment-lat...
Fichiers produits par l'(les) auteur(s)

Licence


Distributed under a Creative Commons Paternité 4.0 International License

Identifiants

  • HAL Id : hal-01154030, version 2
  • ARXIV : 1505.05983

Citation

Cedric Chauve, Julien Courtiel, Yann Ponty. Counting, generating and sampling tree alignments. ALCOB - 3rd International Conference on Algorithms for Computational Biology - 2016, Jun 2016, Trujillo, Spain. 2016, 〈http://grammars.grlmc.com/AlCoB2016/〉. 〈hal-01154030v2〉

Partager

Métriques

Consultations de
la notice

104

Téléchargements du document

35