Inferring Orthology and Paralogy
Open accessAbstract
The distinction between orthologs and paralogs, genes that started diverging by speciation versus duplication, is relevant in a wide range of contexts, most notably phylogenetic tree inference and protein function annotation. In this chapter, we provide an overview of the methods used to infer orthology and paralogy. We survey both graph-based approaches (and their various grouping strategies) and tree-based approaches, which solve the more general problem of gene/species tree reconciliation. We discuss conceptual differences among the various orthology inference methods and databases and examine the difficult issue of verifying and benchmarking orthology predictions. Finally, we review typical applications of orthologous genes, groups, and reconciled trees and conclude with thoughts on future methodological developments.
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Current methods for orthology inference are either based on graph or gene tree approaches or a combination of both.
“Current methods for orthology inference are either based on graph or gene tree approaches or a combination of both (7).”
From Integrating gene annotation with orthology inference at scale (2023) · cites this paper as [7]
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Genome-scale approaches to resolving incongruence in molecular phylogenies.
Rokas, A., Williams, B. L., King, N., & Carroll, S. B. (2003) · Nature · doi:10.1038/nature02053 · Cited by 1,512 · see citing works
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Research works printed but not linked: 15
- Alioto T (2012) Gene prediction. In: Anisi- mova M (ed) Evolutionary genomics: statisti- cal and computational methods, vol 1. Humana, Totowa, NJ, pp 175-201
- Lo ¨ytynoja A (2012) Alignment methods: strategies, challenges, benchmarking, and comparative overview. In: Anisimova M (ed) Evolutionary genomics: statistical and computational methods, vol 1. Humana, Totowa, NJ, pp 203-235
- Chor B, Tuller T (2005) Maximum likelihood of evolutionary trees is hard. In: Proceedings of the 9th annual international conference on research in computational molecular biology. Springer, Berlin, pp 296-310
- Dessimoz C, Cannarozzi G, Gil M et al (2005) OMA, a comprehensive, automated project for the identification of orthologs from complete genome data: introduction and first achievements. In: Comparative geno- mics. Springer, Berlin, pp 61-72
- Van Dongen SM (2001) Graph clustering by flow simulation. PhD thesis, University of Utrecht
- Nei M (1987) Molecular evolutionary genet- ics. Columbia University Press, New York
- Hallett MT, Lagergren J (2000) New algo- rithms for the duplication-loss model. In: Proceedings of the fourth annual interna- tional conference on computational molecular biology. ACM, New York, NY, pp 138-146
- Graybeal A (1998) Is it better to add taxa or characters to a difficult phylogenetic problem? Syst Biol 47(1):9-17
- Doyon J-P, Hamel S, Chauve C (2012) An efficient method for exploring the space of gene tree/species tree reconciliations in a probabilistic framework. IEEE/ACM Trans Comput Biol Bioinform 9:26-39
- Cosentino S, Iwasaki W (2018) SonicPara- noid: extremely fast, accurate, and easy orthology inference. Bioinformatics. https:// doi.org/10.1093/bioinformatics/bty631 · DOI · Paper page
- Steinegger M, So ¨ding J (2017) MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets. Nat Bio- technol 35(11):1026-1028
- Cook SA (1971) The complexity of theorem- proving procedures. In: Proceedings of the third annual ACM symposium on theory of computing. ACM, New York, NY, pp 151-158 105.
- Go ´recki P (2004) Reconciliation problems for duplication, loss and horizontal gene transfer. In: Proceedings of the eighth annual international conference on research in computational molecular biology. ACM, New York, NY, pp 316-325 108.
- Hallett M, Lagergren J, Tofigh A (2004) Simultaneous identification of duplications and lateral transfers. In: Proceedings of the eighth annual international conference on Research in computational molecular biology. ACM, New York, NY, pp 347-356 109.
- Forslund K, Pereira C, Capella-Gutierrez S et al (2017) Gearing up to handle the mosaic nature of life in the quest for orthologs. Bio- informatics. https://doi.org/10.1093/bioin formatics/btx542 110. · DOI
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Integrating gene annotation with orthology inference at scale
Kirilenko, B. M., Munegowda, C., Osipova, E., Jebb, D., Sharma, V., Blumer, M., Morales, A. E., Ahmed, A.-W., Kontopoulos, D.-G., Hilgers, L., et al. (2023) · Science · doi:10.1126/science.abn3107 · Cited by 209 · see citing works
Wenger, Y., & Galliot, B. (2013) · Genome Biology and Evolution · doi:10.1093/gbe/evt142 · Cited by 26 · see citing works
Rivas-Santisteban, J., Yubero, P., Robaina-Estévez, S., González, J. M., Tamames, J., & Pedrós-Alió, C. (2024) · ISME Communications · doi:10.1093/ismeco/ycae042 · Cited by 15 · see citing works
- Authors
- Altenhoff, A. M., Glover, N. M., & Dessimoz, C.
- Affiliations
- SIB Swiss Institute of Bioinformatics (CH)
- Corresponding author
- Dessimoz, Christophe
- Venue
- Methods in Molecular Biology
- Publisher
- Springer New York
- Published
- 2019
- Volume
- 1910
- Pages
- 149-175
- ISSN
- 1064-3745 (ISSN-L)
- 1940-6029
- OpenAlex
- W2901642597
- Cited by
- 148
- References
- 1
- Citations by year
- 2026: 3 · 2025: 12 · 2024: 18 · 2023: 14 · 2022: 9 · 2021: 17 · 2020: 17 · 2019: 6 · 2018: 7 · 2017: 6 · 2016: 6 · 2015: 6 · 2014: 13 · 2013: 9 · 2012: 5
- FWCI
- 13.97
- Type
- book chapter
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Methods in molecular biology (publishedVersion, cc-by)
- PubMed (publishedVersion)
- UCL Discovery (University College London) (submittedVersion)
- IRIS (submittedVersion)
- SERVAL (Université de Lausanne) (submittedVersion)
- Funders
- National Science Foundation
- Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (150654)
- 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 inference, gene duplication, speciation, gene tree reconciliation, phylogenetic inference, protein annotation
- MeSH terms
- Algorithms, Animals, Multigene Family, Humans, Phylogeny, Genome, Evolution, Molecular, Computational Biology, Genomics
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