@inproceedings{8ea606991e6643e0b20899bb731dabd8,
title = "A linear inside-outside algorithm for correcting sequencing errors in structured RNAs",
abstract = "Analysis of the sequence-structure relationship in RNA molecules are essential to evolutionary studies but also to concrete applications such as error-correction methodologies in sequencing technologies. The prohibitive sizes of the mutational and conformational landscapes combined with the volume of data to proceed require efficient algorithms to compute sequence-structure properties. More specifically, here we aim to calculate which mutations increase the most the likelihood of a sequence to a given structure and RNA family. In this paper, we introduce RNApyro, an efficient linear-time and space inside-outside algorithm that computes exact mutational probabilities under secondary structure and evolutionary constraints given as a multiple sequence alignment with a consensus structure. We develop a scoring scheme combining classical stacking base pair energies to novel isostericity scales, and apply our techniques to correct point-wise errors in 5s rRNA sequences. Our results suggest that RNApyro is a promising algorithm to complement existing tools in the NGS error-correction pipeline.",
keywords = "RNA, mutations, secondary structure",
author = "Vladimir Reinharz and Yann Ponty and J{\'e}r{\^o}me Waldisp{\"u}hl",
year = "2013",
month = apr,
day = "3",
doi = "10.1007/978-3-642-37195-0_17",
language = "English",
isbn = "9783642371943",
series = "Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)",
pages = "199--211",
booktitle = "Research in Computational Molecular Biology - 17th Annual International Conference, RECOMB 2013, Proceedings",
note = "17th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2013 ; Conference date: 07-04-2013 Through 10-04-2013",
}