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

### Ronny Lorenz, Christoph Flamm, Ivo Hofacker, Peter Stadler

#### Abstract

RNA folding algorithms, including McCaskillâ€™s partition function algorithm for computing base pairing probabilities, can be extended to N â‰¥ 2 interacting strands by considering all permutations Ï€ of the N strands. For each Ï€, 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 McCaskillâ€™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.

Download#### 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