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Cited by 215Genomics and Phylogenetic StudiesBioinformatics and Genomic NetworksChromosomal and Genetic Variations

OMA 2011: orthology inference among 1000 complete genomes

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Altenhoff, A. M., Schneider, A., Gonnet, G. H., Dessimoz, C.·2011·Nucleic Acids Research
DOI 10.1093/nar/gkq1238PMC PMC3013747
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Abstract

OMA (Orthologous MAtrix) is a database that identifies orthologs among publicly available, complete genomes. Initiated in 2004, the project is at its 11th release. It now includes 1000 genomes, making it one of the largest resources of its kind. Here, we describe recent developments in terms of species covered; the algorithmic pipeline--in particular regarding the treatment of alternative splicing, and new features of the web (OMA Browser) and programming interface (SOAP API). In the second part, we review the various representations provided by OMA and their typical applications. The database is publicly accessible at http://omabrowser.org.

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  • Heuristic analysis of pairwise sequence similarity scores is based on the premise that higher scoring sequence pairs are likely to have diverged more recently than lower scoring sequence pairs.

    “The central premise underlying their use is that higher scoring sequence pairs are likely to have diverged more recently than lower scoring sequence pairs.”

    From OrthoFinder: phylogenetic orthology inference for comparative genomics (2019) · cites this paper as [9]

    The Introduction says OMA compares genes using evolutionary distances, and Algorithmic refinements describes pairwise sequence alignments. Neither section states that higher sequence-similarity scores imply more recent divergence than lower scores. Searches for that premise and for a score–divergence relationship found no passage addressing it. (LLM, conf=0.72)

    Experimental — accuracy not yet measured

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Research works printed but not linked: 31

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Authors
Altenhoff, A. M., Schneider, A., Gonnet, G. H., & Dessimoz, C.
Affiliations
  • ETH Zurich (CH)
  • SIB Swiss Institute of Bioinformatics (CH)
Corresponding author
Dessimoz, C.
ORCID
Venue
Nucleic Acids Research
Publisher
Oxford University Press (OUP)
Published
2010-11-27
Volume
39
Issue
Database
Pages
D289-D294
ISSN
  • 0305-1048 (ISSN-L)
  • 1362-4962
DOI
10.1093/nar/gkq1238
PMC
PMC3013747
OpenAlex
W2048448217
Cited by
215
References
1
Citations by year
2026: 3 · 2025: 5 · 2024: 4 · 2023: 5 · 2022: 4 · 2021: 3 · 2020: 8 · 2019: 13 · 2018: 12 · 2017: 9 · 2016: 13 · 2015: 21 · 2014: 39 · 2013: 33 · 2012: 26
FWCI
9.22
Type
journal article
Language
en
Open access
Licence
Locations
  • Nucleic Acids Research (publishedVersion, cc-by-nc)
  • PubMed Central (publishedVersion, cc-by-nc)
  • PubMed (publishedVersion)
  • Zurich Open Repository and Archive (University of Zurich) (acceptedVersion, other-oa)
  • reroDoc Digital Library (submittedVersion)
  • UCL Discovery (University College London) (submittedVersion)
  • Repository for Publications and Research Data (ETH Zurich) (submittedVersion, cc-by-nc)
  • Zurich Open Repository and Archive (University of Zurich) (submittedVersion, other-oa)
  • ETH Zürich Research Collection
  • Zurich Open Repository and Archive (University of Zurich)
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
complete genome sequence, alternative splicing, comparative genomics, protein orthologs
MeSH terms
Algorithms, Genes, Phylogeny, User-Computer Interface, Genome, Alternative Splicing, Evolution, Molecular, Databases, Genetic

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