ArticleBioinformatics (Oxford, England)2025
Annotation matters: the effect of structural gene annotation on orthology inference.
Article in Bioinformatics (Oxford, England), 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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10 citing papers in PubMed.
- Genomic Identification and Comparative Characterization of Chemosensory Genes in Two Walnut Pests.Biology · 2026Article
- ROS-Centered Transcriptomic Regulatory Networks Linking Salinity Stress, Antioxidant Defense and Processability Traits inCurrent issues in molecular biology · 2026Review
- A High-quality Reference Genome and Tissue Expression Atlas for the European Lobster (Homarus gammarus).Genome biology and evolution · 2026Article
- The Paipu framework enables creation of a large-scale mammalian cancer transcriptomics atlas.bioRxiv : the preprint server for biology · 2026Article
- Article
- Towards an evolutionary baseline model ofbioRxiv : the preprint server for biology · 2025Article
- Quest for Orthologs in the era of Data Deluge and AI: Challenges and Innovations in Orthology Prediction and Data Integration.Journal of molecular evolution · 2025Review
- NCBI Orthologs: Public Resource and Scalable Method for Computing High-Precision Orthologs Across Eukaryotic Genomes.Journal of molecular evolution · 2025Article
- Reconstructing Evolutionary Histories with Hierarchical Orthologous Groups.Journal of molecular evolution · 2025Review
- Genomes of the entomopathogenic nematode Steinernema hermaphroditum and its associated bacteria.Genetics · 2025Article
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6 authors.
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Abstract
motivationIn silico gene annotation, the process of identifying the genes present in a genome, remains a challenging task. As genome assemblies rapidly increase, the corresponding gene models and repertoires often fall short in quality. Despite advances in annotation methods, a lack of community standards means that most published gene annotations result from ad hoc pipelines. As a result, only a few species have nearly complete and accurate gene models. This annotation quality is thought to affect downstream analyses, including orthology inference, often the first step of comparative genomics studies.
resultsWe show that different annotation methods yield markedly distinct orthology inferences. We compared orthology assignments of gene models obtained by four prominent protein-coding gene model sources: the NCBI Eukaryotic Genome Annotation Pipeline, the Ensembl Gene Annotation System, the UniProt Reference Proteomes, and Augustus 3.4 (an ab initio pipeline). We observe significant discrepancies between sources, namely in the proportion of orthologous genes per genome, the completeness of Hierarchical Orthologous Groups, and the accuracy and recall of the predicted orthologs on a standard orthology benchmark.
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