TY - GEN
T1 - Bi-alignments as models of incongruent evolution of RNA sequence and secondary structure
AU - Waldl, Maria
AU - Will, Sebastian
AU - Wolfinger, Michael T.
AU - Hofacker, Ivo L.
AU - Stadler, Peter F.
N1 - Publisher Copyright:
© Springer Nature Switzerland AG 2020.
PY - 2020/1/1
Y1 - 2020/1/1
N2 - 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. Bi-alignments 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.
AB - 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. Bi-alignments 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.
KW - 4-way alignment
KW - Incongruent evolution
KW - RNA alignment
KW - RNA secondary structure
UR - https://www.scopus.com/pages/publications/85098292680
U2 - 10.1007/978-3-030-63061-4_15
DO - 10.1007/978-3-030-63061-4_15
M3 - Conference contribution
AN - SCOPUS:85098292680
SN - 9783030630607
T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
SP - 159
EP - 170
BT - Computational Intelligence Methods for Bioinformatics and Biostatistics - 16th International Meeting, CIBB 2019, Revised Selected Papers
A2 - Cazzaniga, Paolo
A2 - Besozzi, Daniela
A2 - Merelli, Ivan
A2 - Manzoni, Luca
PB - Springer Science and Business Media Deutschland GmbH
T2 - 16th International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics, CIBB 2019
Y2 - 4 September 2019 through 6 September 2019
ER -