  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 and 16s rRNA sequences. Our
results suggest that RNApyro is a promising algorithm to complement existing
tools in the NGS error-correction pipeline.
