A linear inside-outside algorithm for correcting sequencing errors in structured RNA sequences

Vladimir Reinharz (1) , Yann Ponty (2, 3) , Jérôme Waldispühl (4)

1 MCB - McGill Centre for Bioinformatics
2 LIX - Laboratoire d'informatique de l'École polytechnique [Palaiseau]
3 AMIB - Algorithms and Models for Integrative Biology
4 McGill University = Université McGill [Montréal, Canada]

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 e cient algorithms to compute sequence-structure properties. More speci cally, 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 e cient 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.

Domaines: Bio-informatique [q-bio.QM]; Bio-Informatique, Biologie Systémique [q-bio.QM]

Vladimir Reinharz, Yann Ponty, Jérôme Waldispühl. A linear inside-outside algorithm for correcting sequencing errors in structured RNA sequences. RECOMB - 17th Annual International Conference on Research in Computational Molecular Biology - 2013, Apr 2013, Beijing, China. ⟨hal-00766781⟩