Joining forces in the quest for orthologs
Open accessAbstract
Better orthology-prediction resources would be beneficial for the whole biological community. A recent meeting discussed how to coordinate and leverage current efforts.
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QfO is the most widely used orthology benchmarking service, evaluating a tool's ability to accurately predict orthologs across diverse taxa.
“QfO is the most widely used orthology benchmarking service, which evaluates a tool’s ability to accurately predict orthologs across a diverse set of taxa, including Archaea, Bacteria and eukaryotes.”
From OrthoFinder: improved phylogenetic orthology inference with enhanced accuracy and scalability (2026) · cites this paper as [2]
The sections on benchmarking orthology-prediction methods and standardized protein datasets discuss assessing prediction methods and propose a dataset spanning a wide range of evolutionary distances (pages unavailable). They do not describe an operating QfO benchmarking service, establish that it is the most widely used, or specify coverage of Archaea, Bacteria, and eukaryotes. (LLM, conf=0.86)
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Research works printed but not linked: 13
- Gabaldón T Large-scale assignment of orthology: back to phylogenetics? Genome Biol 2008 9 235 18983710 10.1186/gb-2008-9-10-235 PMC2760865 · DOI
- Kuzniar A van Ham RC Pongor S Leunissen JA The quest for orthologs: finding the corresponding gene across genomes. Trends Genet 2008 24 539 551 18819722 10.1016/j.tig.2008.08.009 · DOI
- Alexeyenko A Lindberg J Perez-Bercoff A Sonnhammer EL Overview and comparison of ortholog databases. Drug Disc Today: Technologies 2006 3 137 143 10.1016/j.ddtec.2006.06.002 24980400 · DOI
- Datta RS Meacham C Samad B Neyer C Sjolander K Berkeley PHOG: PhyloFacts orthology group prediction web server. Nucleic Acids Res 2009 37 Web Server W84 W89 19435885 10.1093/nar/gkp373 PMC2703887 · DOI
- Jensen LJ Julien P Kuhn M von Mering C Muller J Doerks T Bork P eggNOG: automated construction and annotation of orthologous groups of genes. Nucleic Acids Res 2008 36 Database D250 D254 17942413 PMC2238944
- Uchiyama I MBGD: a platform for microbial comparative genomics based on the automated construction of orthologous groups. Nucleic Acids Res 2007 35 Database D343 D346 17135196 10.1093/nar/gkl978 PMC1751538 · DOI
- Roth AC Gonnet GH Dessimoz C Algorithm of OMA for large-scale orthology inference. BMC Bioinformatics 2008 9 518 19055798 10.1186/1471-2105-9-518 PMC2639434 · DOI
- Fitch WM Distinguishing homologous from analogous proteins. Syst Zool 1970 19 99 113 5449325 10.2307/2412448 · DOI · Paper page
- Altenhoff AM Dessimoz C Phylogenetic and functional assessment of orthologs inference projects and methods. PLoS Comput Biol 2009 5 e1000262 19148271 10.1371/journal.pcbi.1000262 PMC2612752 · DOI
- Chen F Mackey AJ Vermunt JK Roos DS Assessing performance of orthology detection strategies applied to eukaryotic genomes. PLoS One 2007 2 e383 17440619 10.1371/journal.pone.0000383 PMC1849888 · DOI
- Hulsen T Huynen MA de Vlieg J Groenen PM Benchmarking ortholog identification methods using functional genomics data. Genome Biol 2006 7 R31 16613613 10.1186/gb-2006-7-4-r31 PMC1557999 · DOI
- Bruford EA Lush MJ Wright MW Sneddon TP Povey S Birney E The HGNC Database in 2008: a resource for the human genome. Nucleic Acids Res 2008 36 Database D445 D448 17984084 PMC2238870
- Kuzniar A Lin K He Y Nijveen H Pongor S Leunissen JA ProGMap: an integrated annotation resource for protein orthology. Nucleic Acids Res 2009 37 Web Server W428 W434 19494185 10.1093/nar/gkp462 PMC2703891 · DOI
Cited by
Sorted by citations
Advances and Applications in the Quest for Orthologs
Glover, N., Dessimoz, C., Ebersberger, I., Forslund, S. K., Gabaldón, T., Huerta-Cepas, J., Martin, M.-J., Muffato, M., Patricio, M., Pereira, C., et al. (2019) · Molecular Biology and Evolution · doi:10.1093/molbev/msz150 · Cited by 94 · see citing works
Self-citationOrthoFinder: improved phylogenetic orthology inference with enhanced accuracy and scalability
Emms, D. M., Liu, Y., Belcher, L., Holmes, J., & Kelly, S. (2026) · Nature Methods · doi:10.1038/s41592-026-03126-6 · Cited by 25 · see citing works
- Authors
- Gabaldón, T., Dessimoz, C., Huxley-Jones, J., Vilella, A. J., Sonnhammer, E. L., & Lewis, S.
- Affiliations
- Centre for Genomic Regulation (ES)
- SIB Swiss Institute of Bioinformatics (CH)
- European Bioinformatics Institute (GB)
- Stockholm University (SE)
- Lawrence Berkeley National Laboratory (US)
- Corresponding author
- Gabaldón, Toni
- Venue
- Genome Biology
- Published
- 2009
- Volume
- 10
- Issue
- 9
- Pages
- 403
- ISSN
- 1465-6906 (ISSN-L)
- PMC
- PMC2768974
- OpenAlex
- W2146709375
- Cited by
- 74
- References
- 0
- Citations by year
- 2026: 1 · 2025: 1 · 2024: 1 · 2023: 1 · 2022: 2 · 2021: 1 · 2020: 4 · 2019: 4 · 2018: 3 · 2017: 1 · 2016: 5 · 2015: 5 · 2014: 6 · 2013: 10 · 2012: 8
- FWCI
- 3.62
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Genome biology (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- UCL Discovery (University College London) (submittedVersion)
- Funders
- Wellcome Trust
- European Science Foundation
- 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 › Molecular Biology › Biomedical Text Mining and Ontologies
- Keywords
- ortholog prediction, orthology, comparative genomics, bioinformatics resources, community coordination
- MeSH terms
- Animals, Humans, Phylogeny, Proteins, Technology Transfer, Computational Biology, Genomics, Proteomics
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