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Nucleic Acids Res. 2018 Jan 4;46(D1):D477-D485. doi: 10.1093/nar/gkx1019.

The OMA orthology database in 2018: retrieving evolutionary relationships among all domains of life through richer web and programmatic interfaces.

Author information

1
SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.
2
ETH Zurich, Computer Science, Universitätstrasse 6, 8092 Zurich, Switzerland.
3
Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland.
4
Dept. of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland.
5
Dept. of Genetics, Evolution & Environment, University College London, Gower St, London WC1E 6BT, UK.
6
Bayer Crop Science NV, Technologiepark 38, 9052 Gent, Belgium.
7
Dept. of Computer Science, University College London, Gower St, London WC1E 6BT, UK.

Abstract

The Orthologous Matrix (OMA) is a leading resource to relate genes across many species from all of life. In this update paper, we review the recent algorithmic improvements in the OMA pipeline, describe increases in species coverage (particularly in plants and early-branching eukaryotes) and introduce several new features in the OMA web browser. Notable improvements include: (i) a scalable, interactive viewer for hierarchical orthologous groups; (ii) protein domain annotations and domain-based links between orthologous groups; (iii) functionality to retrieve phylogenetic marker genes for a subset of species of interest; (iv) a new synteny dot plot viewer; and (v) an overhaul of the programmatic access (REST API and semantic web), which will facilitate incorporation of OMA analyses in computational pipelines and integration with other bioinformatic resources. OMA can be freely accessed at https://omabrowser.org.

PMID:
29106550
PMCID:
PMC5753216
DOI:
10.1093/nar/gkx1019
[Indexed for MEDLINE]
Free PMC Article

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