Efficient Computation of Base-pairing Probabilities in Multi-strand RNA Folding

Ronny Lorenz, Christoph Flamm, Ivo L. Hofacker, Ivo L. Hofacker, Peter F. Stadler, Peter F. Stadler, Peter F. Stadler, Peter F. Stadler, Peter F. Stadler

2020

Abstract

RNA folding algorithms, including McCaskill’s partition function algorithm for computing base pairing probabilities, can be extended to N ≥ 2 interacting strands by considering all permutations π of the N strands. For each π, the inside dynamic programming recursion for connected structures needs to be extended by only a single extra case corresponding to a base pair connecting exactly two connected substructures. This leaves the cubic running time unchanged. A straightforward implementation of the corresponding outside recursion, however results in a quartic algorithm. We show here how cubic running time asymptotically equal to McCaskill’s partition function algorithm can be achieved by introducing linear-size auxiliary arrays. The algorithm is implemented within the framework of the ViennaRNA package and conforms to the theoretical performance bounds.

Paper Citation

in Harvard Style

Lorenz R., Flamm C., Hofacker I. and Stadler P. (2020). Efficient Computation of Base-pairing Probabilities in Multi-strand RNA Folding. In Proceedings of the 13th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2020) - Volume 3: BIOINFORMATICS; ISBN 978-989-758-398-8, SciTePress, pages 23-31. DOI: 10.5220/0008916600230031

in Bibtex Style

@conference{bioinformatics20,
author={Ronny Lorenz and Christoph Flamm and Ivo L. Hofacker and Peter F. Stadler},
title={Efficient Computation of Base-pairing Probabilities in Multi-strand RNA Folding},
booktitle={Proceedings of the 13th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2020) - Volume 3: BIOINFORMATICS},
year={2020},
pages={23-31},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0008916600230031},
isbn={978-989-758-398-8},
}

in EndNote Style

TY - CONF

JO - Proceedings of the 13th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2020) - Volume 3: BIOINFORMATICS
TI - Efficient Computation of Base-pairing Probabilities in Multi-strand RNA Folding
SN - 978-989-758-398-8
AU - Lorenz R.
AU - Flamm C.
AU - Hofacker I.
AU - Stadler P.
PY - 2020
SP - 23
EP - 31
DO - 10.5220/0008916600230031
PB - SciTePress