A Linear Inside-Outside Algorithm for Correcting Sequencing Errors in Structured RNAs

  • Vladimir Reinharz
  • Yann Ponty
  • Jérôme Waldispühl
Part of the Lecture Notes in Computer Science book series (LNCS, volume 7821)

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 

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Copyright information

© Springer-Verlag Berlin Heidelberg 2013

Authors and Affiliations

  • Vladimir Reinharz
    • 1
  • Yann Ponty
    • 2
  • Jérôme Waldispühl
    • 1
  1. 1.School of Computer ScienceMcGill UniversityMontrealCanada
  2. 2.Laboratoire d’informatiqueÉcole PolytechniquePalaiseauFrance

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