A Combinatorial Framework for Designing (Pseudoknotted) RNA Algorithms - Archive ouverte HAL Access content directly
Conference Papers Year : 2011

A Combinatorial Framework for Designing (Pseudoknotted) RNA Algorithms

(1, 2) , (1, 3, 4)
1
2
3
4

Abstract

We extend an hypergraph representation, introduced by Finkelstein and Roytberg, to unify dynamic programming algorithms in the context of RNA folding with pseudoknots. Classic applications of RNA dynamic programming energy minimization, partition function, base-pair probabilities\ldots) are reformulated within this framework, giving rise to very simple algorithms. This reformulation allows one to conceptually detach the conformation space/energy model -- captured by the hypergraph model -- from the specific application, assuming unambiguity of the decomposition. To ensure the latter property, we propose a new combinatorial methodology based on generating functions. We extend the set of generic applications by proposing an exact algorithm for extracting generalized moments in weighted distribution, generalizing a prior contribution by Miklos and al. Finally, we illustrate our full-fledged programme on three exemplary conformation spaces (secondary structures, Akutsu's simple type pseudoknots and kissing hairpins). This readily gives sets of algorithms that are either novel or have complexity comparable to classic implementations for minimization and Boltzmann ensemble applications of dynamic programming.
Fichier principal
Vignette du fichier
BoltzmannEnsembleWithPK.pdf (707.09 Ko) Télécharger le fichier
Origin : Files produced by the author(s)
Loading...

Dates and versions

inria-00601060 , version 1 (19-06-2011)

Identifiers

  • HAL Id : inria-00601060 , version 1
  • ARXIV : 1106.3771

Cite

Yann Ponty, Cédric Saule. A Combinatorial Framework for Designing (Pseudoknotted) RNA Algorithms. WABI - 11th Workshop on Algorithms in Bioinformatics - 2011, 2011, Saarbrucken, Germany. ⟨inria-00601060⟩
313 View
394 Download

Altmetric

Share

Gmail Facebook Twitter LinkedIn More