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Bi-alignments as Models of Incongruent Evolution of RNA Sequence and Secondary Structure

Abstract : RNA molecules may be subject to independent selection pressures on sequence and structure. This can, in principle, lead to the preservation of structural features without maintaining the exact position on the conserved sequence. Consequently, structurally analogous base pairs are no longer formed by homologous bases, and homologous nucleotides do not preserve their structural context. In other words, the evolution of sequence and structure is incongruent. We model this phenomenon by introducing bi-alignments, defined as a pair of alignments, one modeling sequence homology; the other, structural homology, together with an alignment of the two alignments that models the relative shifts between conserved sequence and conserved structure. Bialignments therefore form a special class of four-way alignments. A preliminary survey of the Rfam database suggests that incongruent evolution is not a very rare phenomenon among structured ncRNAs and RNA elements.
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https://hal.inria.fr/hal-03131248
Contributor : Sebastian Will Connect in order to contact the contributor
Submitted on : Thursday, March 25, 2021 - 2:58:26 PM
Last modification on : Thursday, August 12, 2021 - 3:26:53 AM
Long-term archiving on: : Saturday, June 26, 2021 - 6:58:18 PM

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Maria Waldl, Sebastian Will, Peter F. Stadler, Michael T. Wolfinger, Ivo L. Hofacker. Bi-alignments as Models of Incongruent Evolution of RNA Sequence and Secondary Structure. CIBB 2019 - 16th International Conference on Computational Intelligence Methods for Bioinformatics and Biostatistics, Sep 2019, Bergamo, Italy. pp.159-170, ⟨10.1007/978-3-030-63061-4_15⟩. ⟨hal-03131248⟩

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