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Cited by 17Genomics and Phylogenetic StudiesBioinformatics and Genomic NetworksGenome Rearrangement Algorithms

OrthoGNC: A Software for Accurate Identification of Orthologs Based on Gene Neighborhood Conservation

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Jahangiri-Tazehkand, Soheil, Wong, Limsoon, Eslahchi, Changiz·2017·Genomics, Proteomics & Bioinformatics
DOI 10.1016/j.gpb.2017.07.002PMC PMC5828658
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Abstract

Orthology relations can be used to transfer annotations from one gene (or protein) to another. Hence, detecting orthology relations has become an important task in the post-genomic era. Various genomic events, such as duplication and horizontal gene transfer, can cause erroneous assignment of orthology relations. In closely-related species, gene neighborhood information can be used to resolve many ambiguities in orthology inference. Here we present OrthoGNC, a software for accurately predicting pairwise orthology relations based on gene neighborhood conservation. Analyses on simulated and real data reveal the high accuracy of OrthoGNC. In addition to orthology detection, OrthoGNC can be employed to investigate the conservation of genomic context among potential orthologs detected by other methods. OrthoGNC is freely available online at http://bs.ipm.ir/softwares/orthognc and http://tinyurl.com/orthoGNC.

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  • Orthologous chains tend to cover several genes located in a conserved order, resulting in higher synteny values, which can help distinguish orthologs from paralogs.

    “Orthologous chains tend to cover several genes located in a conserved order, resulting in higher synteny values, which can help to distinguish orthologs from paralogs (14, 41–43).”

    From Integrating gene annotation with orthology inference at scale (2023) · cites this paper as [43]

    The Introduction says conserved gene neighborhoods can help distinguish orthologs from out-paralogs, and the Method describes checking multiple neighboring genes, with one routine considering gene order. Our copy does not state that orthologous chains tend to span several genes or that they produce higher synteny values. The indexed passages provide no page numbers. (LLM, conf=0.82)

    Experimental — accuracy not yet measured

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Authors
Jahangiri-Tazehkand, S., Wong, L., & Eslahchi, C.
Affiliations
  • Department of Computer Science, Shahid Beheshti University , Tehran, 1983969411 , Iran
  • National University of Singapore (SG)
  • Shahid Beheshti University (IR)
Corresponding author
Eslahchi, Changiz
ORCID
Venue
Genomics, Proteomics & Bioinformatics
Publisher
Oxford University Press (OUP)
Published
2017-11-11
Volume
15
Issue
6
Pages
361-370
ISSN
  • 1672-0229 (ISSN-L)
  • 2210-3244
DOI
10.1016/j.gpb.2017.07.002
PMC
PMC5828658
OpenAlex
W2767625091
Cited by
17
References
1
Citations by year
2026: 1 · 2025: 4 · 2024: 1 · 2023: 4 · 2022: 1 · 2021: 1 · 2019: 5
FWCI
0.56
Type
journal article
Language
en
Open access
Licence
Locations
  • Genomics Proteomics & Bioinformatics (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • National University of Singapore (submittedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
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 › Biochemistry, Genetics and Molecular Biology › Genetics › Genome Rearrangement Algorithms
Keywords
orthology prediction, annotation transfer, gene duplication, horizontal gene transfer
MeSH terms
Algorithms, Computer Simulation, Genes, Mycobacterium, Phylogeny, Sequence Homology, Nucleic Acid, Software, Time Factors, Conserved Sequence, Proteome, Genomics

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