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Cited by 438Genomics and Phylogenetic StudiesBioinformatics and Genomic NetworksChromosomal and Genetic Variations

OrthoDB v9.1: cataloging evolutionary and functional annotations for animal, fungal, plant, archaeal, bacterial and viral orthologs

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Zdobnov, Evgeny M., Tegenfeldt, Fredrik, Kuznetsov, Dmitry, Waterhouse, Robert M., Simão, Felipe A., Ioannidis, Panagiotis, Seppey, Mathieu, Loetscher, Alexis +1 more·2017·Nucleic Acids Research
DOI 10.1093/nar/gkw1119PMC PMC5210582
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Abstract

OrthoDB is a comprehensive catalog of orthologs, genes inherited by extant species from a single gene in their last common ancestor. In 2016 OrthoDB reached its 9th release, growing to over 22 million genes from over 5000 species, now adding plants, archaea and viruses. In this update we focused on usability of this fast-growing wealth of data: updating the user and programmatic interfaces to browse and query the data, and further enhancing the already extensive integration of available gene functional annotations. Collating functional annotations from over 100 resources, and enabled us to propose descriptive titles for 87% of ortholog groups. Additionally, OrthoDB continues to provide computed evolutionary annotations and to allow user queries by sequence homology. The OrthoDB resource now enables users to generate publication-quality comparative genomics charts, as well as to upload, analyze and interactively explore their own private data. OrthoDB is available from http://orthodb.org.

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  • Graph-based methods cluster genes into pairs or groups of orthologs based on pairwise sequence similarity such as reciprocal best alignment hits.

    “Graph-based methods cluster genes into pairs or groups of orthologs based on pairwise sequence similarity such as (reciprocal) best alignment hits (8–12).”

    From Integrating gene annotation with orthology inference at scale (2023) · cites this paper as [10]

    The Algorithm and Software section (page unavailable) says OrthoDB clusters genes into ortholog groups after Smith–Waterman assessments of gene homology. It does not specify graph-based clustering or reciprocal best alignment hits; searches for those terms found no supporting passage in our copy. (LLM, conf=0.85)

    Experimental — accuracy not yet measured

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Research works printed but not linked: 32

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Cited by

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Authors
Zdobnov, E. M., Tegenfeldt, F., Kuznetsov, D., Waterhouse, R. M., Simão, F. A., Ioannidis, P., Seppey, M., Loetscher, A., & Kriventseva, E. V.
Affiliations
University of Geneva (CH)
Corresponding author
Zdobnov, Evgeny M.
ORCID
Venue
Nucleic Acids Research
Publisher
Oxford University Press (OUP)
Published
2016-11-28
Volume
45
Issue
D1
Pages
D744-D749
ISSN
  • 0305-1048 (ISSN-L)
  • 1362-4962
DOI
10.1093/nar/gkw1119
PMC
PMC5210582
OpenAlex
W2559011563
Cited by
438
References
2
Citations by year
2026: 9 · 2025: 16 · 2024: 21 · 2023: 24 · 2022: 37 · 2021: 80 · 2020: 74 · 2019: 85 · 2018: 72 · 2017: 19 · 2015: 1
FWCI
25.06
Type
journal article
Language
en
Open access
Licence
Locations
  • Nucleic Acids Research (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • Archive ouverte UNIGE (University of Geneva) (publishedVersion, other-oa)
  • HighWire Press Open Archive (submittedVersion)
  • Archive ouverte UNIGE (University of Geneva) (submittedVersion, cc-by)
Funders
Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (143936)
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
OrthoDB, orthologs, orthogroups, gene functional annotation, comparative genomics, sequence homology, archaea, plants, viruses
MeSH terms
Algorithms, Animals, Archaea, Bacteria, Fungi, Plants, Software, User-Computer Interface, Viruses, Evolution, Molecular, Computational Biology, Genomics, Databases, Genetic, Molecular Sequence Annotation, Web Browser

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