ArticleNucleic acids research2013
OrtholugeDB: a bacterial and archaeal orthology resource for improved comparative genomic analysis.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 52 papers.
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Who cites it
52 citing papers in PubMed.
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- 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
- Mycobacterium tuberculosis uses intrinsically disordered, fast evolving proteins to interact with conserved host factors.Genome biology · 2025Article
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- Transfer learning predicts species-specific drug interactions in emerging pathogens.bioRxiv : the preprint server for biology · 2024Article
- ProPan: a comprehensive database for profiling prokaryotic pan-genome dynamics.Nucleic acids research · 2023Article
- Time-Resolved Proteomics of Germinating Spores ofInternational journal of molecular sciences · 2022Article
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- ACDB: An Antibiotic Combination DataBase.Frontiers in pharmacology · 2022Article
- Forecasting of phenotypic and genetic outcomes of experimental evolution in Pseudomonas protegens.PLoS genetics · 2021Article
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- Evolutionary Genomics of Niche-Specific Adaptation to the Cystic Fibrosis Lung in Pseudomonas aeruginosa.Molecular biology and evolution · 2021Article
- Paleogenomic insights into the red complex bacteriaPhilosophical transactions of the Royal Society of London. Series B, Biological sciences · 2020Article
- IpdE1-IpdE2 Is a Heterotetrameric Acyl Coenzyme A Dehydrogenase That Is Widely Distributed in Steroid-Degrading Bacteria.Biochemistry · 2020Article
- An Integrated Multi-Disciplinary Perspectivefor Addressing Challenges of the Human Gut Microbiome.Metabolites · 2020Review
- Article
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Authors and funding
4 authors.
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Abstract
Prediction of orthologs (homologous genes that diverged because of speciation) is an integral component of many comparative genomics methods. Although orthologs are more likely to have similar function versus paralogs (genes that diverged because of duplication), recent studies have shown that their degree of functional conservation is variable. Also, there are inherent problems with several large-scale ortholog prediction approaches. To address these issues, we previously developed Ortholuge, which uses phylogenetic distance ratios to provide more precise ortholog assessments for a set of predicted orthologs. However, the original version of Ortholuge required manual intervention and was not easily accessible; therefore, we now report the development of OrtholugeDB, available online at http://www.pathogenomics.sfu.ca/ortholugedb. OrtholugeDB provides ortholog predictions for completely sequenced bacterial and archaeal genomes from NCBI based on reciprocal best Basic Local Alignment Search Tool hits, supplemented with further evaluation by the more precise Ortholuge method. The OrtholugeDB web interface facilitates user-friendly and flexible ortholog analysis, from single genes to genomes, plus flexible data download options. We compare Ortholuge with similar methods, showing how it may more consistently identify orthologs with conserved features across a wide range of taxonomic distances. OrtholugeDB facilitates rapid, and more accurate, bacterial and archaeal comparative genomic analysis and large-scale ortholog predictions.
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