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Cited by 221Genomics and Phylogenetic StudiesBioinformatics and Genomic NetworksChromosomal and Genetic Variations

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

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Altenhoff, Adrian M, Glover, Natasha M, Train, Clément-Marie, Kaleb, Klara, Warwick Vesztrocy, Alex, Dylus, David, de Farias, Tarcisio M, Zile, Karina +5 more·2018·Nucleic Acids Research
DOI 10.1093/nar/gkx1019PMC PMC5753216
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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.

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Authors
Altenhoff, A. M., Glover, N. M., Train, C.-M., Kaleb, K., Warwick Vesztrocy, A., Dylus, D., de Farias, T. M., Zile, K., Stevenson, C., Long, J., Redestig, H., Gonnet, G. H., & Dessimoz, C.
Affiliations
  • SIB Swiss Institute of Bioinformatics (CH)
  • University College London (GB)
  • Bayer (Belgium) (BE)
Corresponding author
Dessimoz, Christophe
ORCID
Venue
Nucleic Acids Research
Publisher
Oxford University Press (OUP)
Published
2017-11-02
Volume
46
Issue
D1
Pages
D477-D485
ISSN
  • 0305-1048 (ISSN-L)
  • 1362-4962
DOI
10.1093/nar/gkx1019
PMC
PMC5753216
OpenAlex
W2766510537
Cited by
221
References
2
Citations by year
2026: 5 · 2025: 4 · 2024: 7 · 2023: 16 · 2022: 22 · 2021: 41 · 2020: 69 · 2019: 37 · 2018: 19
FWCI
13.61
Type
journal article
Language
en
Open access
Licence
Locations
  • Nucleic Acids Research (publishedVersion, cc-by)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • SERVAL (Université de Lausanne) (publishedVersion, other-oa)
  • IRIS (submittedVersion, other-oa)
  • UCL Discovery (University College London) (submittedVersion)
  • Repository for Publications and Research Data (ETH Zurich) (submittedVersion, cc-by)
  • ETH Zürich Research Collection (cc-by)
Funders
  • University College London
  • Eidgenössische Technische Hochschule Zürich
  • Université de Lausanne
  • Directorate for Biological Sciences
  • Biotechnology and Biological Sciences Research Council (1618923, BB/M009513/1, BB/L018241/1)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
  • Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
Keywords
orthogroups, gene orthology, phylogenetic relationships, protein domain annotation, REST API, semantic web, web browser interface, plants
MeSH terms
Protein Domains, Algorithms, Animals, Archaea, Bacteria, Biological Evolution, Fungi, Humans, Phylogeny, Plants, Proteins, Genome, Computational Biology, Internet, Synteny, Databases, Genetic, Molecular Sequence Annotation, Gene Ontology, Web Browser

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