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Analysis of the sequence-structure relationship in RNA molecules areessential to evolutionary studies but also to concrete applications such aserror-correction methodologies in sequencing technologies. The prohibitivesizes of the mutational and conformational landscapes combined with the volumeof data to proceed require efficient algorithms to compute sequence-structureproperties. More specifically, here we aim to calculate which mutationsincrease the most the likelihood of a sequence to a given structure and RNAfamily. In this paper, we introduce RNApyro, an efficient linear-time and spaceinside-outside algorithm that computes exact mutational probabilities undersecondary structure and evolutionary constraints given as a multiple sequencealignment with a consensus structure. We develop a scoring scheme combiningclassical stacking base pair energies to novel isostericity scales, and applyour techniques to correct point-wise errors in 5s and 16s rRNA sequences. Ourresults suggest that RNApyro is a promising algorithm to complement existingtools in the NGS error-correction pipeline.

Using structural and evolutionary information to detect and correct pyrosequencing errors in non-coding RNAs