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Life 2017, 7(4), 42; doi:10.3390/life7040042

SMORE: Synteny Modulator of Repetitive Elements

1
Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Germany
2
Max Planck Institute for Mathematics in the Sciences, Inselstraße 22, D-04103 Leipzig, Germany
3
Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
4
German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Competence Center for Scalable Data Services and Solutions, and Leipzig Research Center for Civilization Diseases, University Leipzig, D-04103 Leipzig, Germany
5
Fraunhofer Institute for Cell Therapy and Immunology, Perlickstrasse 1, D-04103 Leipzig, Germany
6
Institute for Theoretical Chemistry, University of Vienna, Währingerstraße 17, A-1090 Wien, Austria
7
Center for RNA in Technology and Health, Univ. Copenhagen, Grønnegårdsvej 3, DK-1870 Frederiksberg C, Denmark
8
Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM 87501, USA
*
Author to whom correspondence should be addressed.
Received: 28 August 2017 / Revised: 27 October 2017 / Accepted: 28 October 2017 / Published: 31 October 2017
(This article belongs to the Section Life Sciences)
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Abstract

Several families of multicopy genes, such as transfer ribonucleic acids (tRNAs) and ribosomal RNAs (rRNAs), are subject to concerted evolution, an effect that keeps sequences of paralogous genes effectively identical. Under these circumstances, it is impossible to distinguish orthologs from paralogs on the basis of sequence similarity alone. Synteny, the preservation of relative genomic locations, however, also remains informative for the disambiguation of evolutionary relationships in this situation. In this contribution, we describe an automatic pipeline for the evolutionary analysis of such cases that use genome-wide alignments as a starting point to assign orthology relationships determined by synteny. The evolution of tRNAs in primates as well as the history of the Y RNA family in vertebrates and nematodes are used to showcase the method. The pipeline is freely available. View Full-Text
Keywords: bioinformatics; pipeline; workflow; concerted evolution; synteny; orthology; tandem duplications; Y RNAs; tRNAs bioinformatics; pipeline; workflow; concerted evolution; synteny; orthology; tandem duplications; Y RNAs; tRNAs
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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MDPI and ACS Style

Berkemer, S.J.; Hoffmann, A.; Murray, C.R.A.; Stadler, P.F. SMORE: Synteny Modulator of Repetitive Elements. Life 2017, 7, 42.

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