Bi-Alignments as Models of Incongruent Evolution of RNA Sequence and Structure

Bi-Alignments as Models of Incongruent Evolution of RNA Sequence and Structure

Abstract

RNA molecules may experience independent selection pressures on their sequence and secondary)structure. Structural features then may be preserved without maintaining their exact position along the sequence. In such cases, corresponding base pairs are no longer formed by homologous bases, leading to the incongruent evolutionary conservation of sequence and structure. In order to model this phenomenon, we introduce bi-alignments as a superposition of two alignments: one modeling sequence homology; the other, structural homology. We show that under natural assumptions on the scoring functions, bi-alignments form a special case of 4-way alignments, in which the incongruencies are measured as indels in the pairwise alignment of the two alignment copies. A preliminary survey of the Rfam database suggests that incongruent evolution of RNAs is not a very rare phenomenon.

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Authors
  • Waldl, Maria
  • Will, Sebastian
  • Wolfinger, Michael T.
  • Hofacker, Ivo L.
  • Stadler, Peter F.
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Shortfacts
Category
Paper in Conference Proceedings or in Workshop Proceedings (Paper)
Event Title
CIBB 2019: 16th International Conference on Computational Intelligence methods for Bioinformatics and Biostatistics
Divisions
Bioinformatics and Computational Biology
Event Location
Bergamo. Italy
Event Type
Conference
Event Dates
4-6 September 2019
Date
4 September 2019
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