%0 Conference Proceedings %T Bi-alignments as Models of Incongruent Evolution of RNA Sequence and Secondary Structure %+ Institute for Theoretical Chemistry [Vienna] (ITC) %+ Algorithms and Models for Integrative BIOlogy (AMIBIO) %+ Department of Computer Science [Leipzig] %+ Bioinformatics Group %A Waldl, Maria %A Will, Sebastian %A Stadler, Peter F. %A Wolfinger, Michael T. %A Hofacker, Ivo L. %Z Partial financial support by the German Federal Ministry of Education and Research (BMBF, project no. 031A538A, de.NBI-RBC and 031L0164C, RNAproNET) and the Austrian science fund (FWF project I 2874 “Prediction of RNA-RNA interactions” and doctoral college W 1207 “RNA Biology”) is gratefully acknowledged. %< avec comité de lecture %B CIBB 2019 - 16th International Conference on Computational Intelligence Methods for Bioinformatics and Biostatistics %C Bergamo, Italy %3 Lecture Notes in Computer Science %V 12313 %P 159-170 %8 2019-09-04 %D 2019 %R 10.1007/978-3-030-63061-4_15 %K RNA secondary structure %K RNA alignment %K incongruent evolution %K 4-way alignment %Z Computer Science [cs]/Bioinformatics [q-bio.QM]Conference papers %X 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. %G English %2 https://inria.hal.science/hal-03131248/document %2 https://inria.hal.science/hal-03131248/file/cibb_lnbi.pdf %L hal-03131248 %U https://inria.hal.science/hal-03131248 %~ X %~ CNRS %~ LIX %~ X-LIX %~ X-DEP %~ X-DEP-INFO %~ IP_PARIS %~ IP_PARIS_COPIE