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

Ronny Lorenz, Christoph Flamm, Ivo Hofacker, Peter Stadler

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.

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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 - Volume 3: BIOINFORMATICS, ISBN 978-989-758-398-8, pages 23-31. DOI: 10.5220/0008916600230031


in Bibtex Style

@conference{bioinformatics20,
author={Ronny Lorenz and Christoph Flamm and Ivo Hofacker and Peter 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 - 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 - 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