ArticleBioEssays : news and reviews in molecular, cellular and developmental biology2011
Orthology prediction methods: a quality assessment using curated protein families.
Article in BioEssays : news and reviews in molecular, cellular and developmental biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 80 papers.
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Who cites it
80 citing papers in PubMed.
- Comparative Genomic Analysis Reveals Distribution, Organization, and Evolution of Ferrous and Sulfur Oxidation Genes in the GenusInternational journal of molecular sciences · 2026Article
- OrthoFinder: improved phylogenetic orthology inference with enhanced accuracy and scalability.Nature methods · 2026Article
- Reconstructing Evolutionary Histories with Hierarchical Orthologous Groups.Journal of molecular evolution · 2025Review
- Annotation matters: the effect of structural gene annotation on orthology inference.Bioinformatics (Oxford, England) · 2025Article
- A curated benchmark dataset for molecular identification based on genome skimming.Scientific data · 2025Article
- SCARAP: scalable cross-species comparative genomics of prokaryotes.Bioinformatics (Oxford, England) · 2024Article
- Unraveling genomic features and phylogenomics through the analysis of three Mexican endemicPeerJ · 2024Article
- Integrating gene annotation with orthology inference at scale.Science (New York, N.Y.) · 2023Article
- Article
- OrthoDB v11: annotation of orthologs in the widest sampling of organismal diversity.Nucleic acids research · 2023Article
- ORTHOSCOPE*: A Phylogenetic Pipeline to Infer Gene Histories from Genome-Wide Data.Molecular biology and evolution · 2022Article
- Draft genome assembly for the colombian freshwater bocachico fish,Frontiers in genetics · 2022Article
- Orthology Clusters from Gene Trees with Possvm.Molecular biology and evolution · 2021Article
- KinOrtho: a method for mapping human kinase orthologs across the tree of life and illuminating understudied kinases.BMC bioinformatics · 2021Article
- Evolution of Microbial Genomics: Conceptual Shifts over a Quarter Century.Trends in microbiology · 2021Review
- OrthoDB in 2020: evolutionary and functional annotations of orthologs.Nucleic acids research · 2021Article
- Benchmarking Orthogroup Inference Accuracy: Revisiting Orthobench.Genome biology and evolution · 2020Article
- The genetic factors of bilaterian evolution.eLife · 2020Article
- Phylogenetic tree building in the genomic age.Nature reviews. Genetics · 2020Review
- Genome-Scale Characterization of Predicted Plastid-Targeted Proteomes in Higher Plants.Scientific reports · 2020Article
20 more citing papers are in PubMed but not listed here.
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Authors and funding
7 authors.
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No grant is acknowledged in the PubMed record.
Abstract
The increasing number of sequenced genomes has prompted the development of several automated orthology prediction methods. Tests to evaluate the accuracy of predictions and to explore biases caused by biological and technical factors are therefore required. We used 70 manually curated families to analyze the performance of five public methods in Metazoa. We analyzed the strengths and weaknesses of the methods and quantified the impact of biological and technical challenges. From the latter part of the analysis, genome annotation emerged as the largest single influencer, affecting up to 30% of the performance. Generally, most methods did well in assigning orthologous group but they failed to assign the exact number of genes for half of the groups. The publicly available benchmark set (http://eggnog.embl.de/orthobench/) should facilitate the improvement of current orthology assignment protocols, which is of utmost importance for many fields of biology and should be tackled by a broad scientific community.
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