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Creative Commons Attribution 4.0 International license (CC BY 4.0)
When quoting this document, please refer to the following
DOI: 10.4230/LIPIcs.WABI.2023.19
URN: urn:nbn:de:0030-drops-186454
URL: http://dagstuhl.sunsite.rwth-aachen.de/volltexte/2023/18645/
Gray, Mateo ;
Will, Sebastian ;
Jabbari, Hosna
SparseRNAFolD: Sparse RNA Pseudoknot-Free Folding Including Dangles
Abstract
Motivation. Computational RNA secondary structure prediction by free energy minimization is indispensable for analyzing structural RNAs and their interactions. These methods find the structure with the minimum free energy (MFE) among exponentially many possible structures and have a restrictive time and space complexity (O(n³) time and O(n²) space for pseudoknot-free structures) for longer RNA sequences. Furthermore, accurate free energy calculations, including dangles contributions can be difficult and costly to implement, particularly when optimizing for time and space requirements.
Results. Here we introduce a fast and efficient sparsified MFE pseudoknot-free structure prediction algorithm, SparseRNAFolD, that utilizes an accurate energy model that accounts for dangle contributions. While the sparsification technique was previously employed to improve the time and space complexity of a pseudoknot-free structure prediction method with a realistic energy model, SparseMFEFold, it was not extended to include dangle contributions due to the complexity of computation. This may come at the cost of prediction accuracy. In this work, we compare three different sparsified implementations for dangles contributions and provide pros and cons of each method. As well, we compare our algorithm to LinearFold, a linear time and space algorithm, where we find that in practice, SparseRNAFolD has lower memory consumption across all lengths of sequence and a faster time for lengths up to 1000 bases.
Conclusion. Our SparseRNAFolD algorithm is an MFE-based algorithm that guarantees optimality of result and employs the most general energy model, including dangle contributions. We provide a basis for applying dangles to sparsified recursion in a pseudoknot-free model that has the ability to be extended to pseudoknots.
BibTeX - Entry
@InProceedings{gray_et_al:LIPIcs.WABI.2023.19,
author = {Gray, Mateo and Will, Sebastian and Jabbari, Hosna},
title = {{SparseRNAFolD: Sparse RNA Pseudoknot-Free Folding Including Dangles}},
booktitle = {23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)},
pages = {19:1--19:18},
series = {Leibniz International Proceedings in Informatics (LIPIcs)},
ISBN = {978-3-95977-294-5},
ISSN = {1868-8969},
year = {2023},
volume = {273},
editor = {Belazzougui, Djamal and Ouangraoua, A\"{i}da},
publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
address = {Dagstuhl, Germany},
URL = {https://drops.dagstuhl.de/opus/volltexte/2023/18645},
URN = {urn:nbn:de:0030-drops-186454},
doi = {10.4230/LIPIcs.WABI.2023.19},
annote = {Keywords: RNA, MFE, Secondary Structure Prediction, Dangle, Sparsification, Space Complexity, Time Complexity}
}
