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Methods Mol Biol. 2018;1704:363-400. doi: 10.1007/978-1-4939-7463-4_14.

Comparative RNA Genomics.

Backofen R1,2, Gorodkin J2, Hofacker IL2,3,4, Stadler PF5,6,7,8,9,10.

Author information

1
Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Köhler-Allee 106, D-79110 Freiburg, Germany.
2
Center for non-coding RNA in Technology and Health, Department of Veterinary and Animal Sciences, University of Copenhagen, Grønnegårdsvej 3, DK-1870 Frederiksberg C, Denmark.
3
Institute for Theoretical Chemistry, University of Vienna, Währingerstraße 17, A-1090 Wien, Austria.
4
Bioinformatics and Computational Biology Research Group, University of Vienna, Währingerstraße 17, A-1090 Vienna, Austria.
5
Center for non-coding RNA in Technology and Health, Department of Veterinary and Animal Sciences, University of Copenhagen, Grønnegårdsvej 3, DK-1870 Frederiksberg C, Denmark. studla@bioinf.uni-leipzig.de.
6
Institute for Theoretical Chemistry, University of Vienna, Währingerstraße 17, A-1090 Wien, Austria. studla@bioinf.uni-leipzig.de.
7
Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Germany. studla@bioinf.uni-leipzig.de.
8
Max Planck Institute for Mathematics in the Sciences, Inselstraße 22, D-04103 Leipzig, Germany. studla@bioinf.uni-leipzig.de.
9
Fraunhofer Institute for Cell Therapy and Immunology, Perlickstraße 1, D-04103 Leipzig, Germany. studla@bioinf.uni-leipzig.de.
10
Santa Fe Institute, 1399 Hyde Park Rd, Santa Fe, NM 87501, USA. studla@bioinf.uni-leipzig.de.

Abstract

Over the last two decades it has become clear that RNA is much more than just a boring intermediate in protein expression. Ancient RNAs still appear in the core information metabolism and comprise a surprisingly large component in bacterial gene regulation. A common theme with these types of mostly small RNAs is their reliance of conserved secondary structures. Large scale sequencing projects, on the other hand, have profoundly changed our understanding of eukaryotic genomes. Pervasively transcribed, they give rise to a plethora of large and evolutionarily extremely flexible noncoding RNAs that exert a vastly diverse array of molecule functions. In this chapter we provide a-necessarily incomplete-overview of the current state of comparative analysis of noncoding RNAs, emphasizing computational approaches as a means to gain a global picture of the modern RNA world.

KEYWORDS:

Alternative splicing; Chromatin; Evolution; Long noncoding RNA; RNA secondary structure

PMID:
29277874
DOI:
10.1007/978-1-4939-7463-4_14
[Indexed for MEDLINE]

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