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J Biotechnol. 2017 Nov 10;261:97-104. doi: 10.1016/j.jbiotec.2017.07.007. Epub 2017 Jul 8.

Recent advances in RNA folding.

Author information

1
Bioinformatics Group, Department of Computer Science; and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Germany.
2
Institute for Theoretical Chemistry, University of Vienna, Währingerstraße 17, A-1090 Wien, Austria.
3
Bioinformatics, University of Freiburg, Georges-Köhler-Allee 106, 79110 Freiburg, Germany.
4
Bioinformatics Group, Department of Computer Science; and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Germany; Institute for Theoretical Chemistry, University of Vienna, Währingerstraße 17, A-1090 Wien, Austria; RNomics Group, Fraunhofer Institute for Cell Therapy and Immunology, Perlickstraße 1, 04103, Leipzig, Germany; Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM 87501, USA. Electronic address: studla@bioinf.uni-leipzig.de.

Abstract

In the realm of nucleic acid structures, secondary structure forms a conceptually important intermediate level of description and explains the dominating part of the free energy of structure formation. Secondary structures are well conserved over evolutionary time-scales and for many classes of RNAs evolve slower than the underlying primary sequences. Given the close link between structure and function, secondary structure is routinely used as a basis to explain experimental findings. Recent technological advances, finally, have made it possible to assay secondary structure directly using high throughput methods. From a computational biology point of view, secondary structures have a special role because they can be computed efficiently using exact dynamic programming algorithms. In this contribution we provide a short overview of RNA folding algorithms, recent additions and variations and address methods to align, compare, and cluster RNA structures, followed by a tabular summary of the most important software suites in the fields.

KEYWORDS:

RNA analysis; RNA constraint folding; RNA interactions; RNA secondary structure; RNA secondary structure comparison

PMID:
28690134
DOI:
10.1016/j.jbiotec.2017.07.007
[Indexed for MEDLINE]
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