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.
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Reinharz, V., Ponty, Y., Waldispühl, J. (2013). A Linear Inside-Outside Algorithm for Correcting Sequencing Errors in Structured RNAs. In: Deng, M., Jiang, R., Sun, F., Zhang, X. (eds) Research in Computational Molecular Biology. RECOMB 2013. Lecture Notes in Computer Science(), vol 7821. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-37195-0_17
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DOI: https://doi.org/10.1007/978-3-642-37195-0_17
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