ArticleNucleic acids research2024
OMA orthology in 2024: improved prokaryote coverage, ancestral and extant GO enrichment, a revamped synteny viewer and more in the OMA Ecosystem.
Article in Nucleic acids research, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 62 papers.
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62 citing papers in PubMed.
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- Evolutionary history and recombination in the mitochondrial carrier SLC25 superfamily analyzed by similarities in the exon and transmembrane α-helix sequences.Protein science : a publication of the Protein Society · 2026Article
- An inflammasome-driven differentiation program in intestinal stem cells protects against Salmonella infection.Nature immunology · 2026Article
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- DrosGB: An integrated multi-omics database for comparative genomics and functional annotation of 35hLife · 2026Article
- The vault associates with membranes in situ.Nature communications · 2026Article
- DIOPT: the DRSC Integrative Ortholog Prediction Tool, 2026 update.bioRxiv : the preprint server for biology · 2026Article
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- A highly contiguous genome assembly for the California vole, Microtus californicus, provides insight into phylogenetic relationships and patterns of synteny among voles.The Journal of heredity · 2026Article
- Cross-species gene redesign leveraging ortholog information and generative modeling.Nature communications · 2026Article
- A hot origin of dissimilatory sulfite reduction catalyzed by DsrAB in the Paleoarchean Era.mLife · 2026Article
- TogoMCP: natural language querying of life-science knowledge graphs via schema-guided LLMs and the Model Context Protocol.Database : the journal of biological databases and curation · 2026Article
- eggNOG v7: phylogeny-based orthology predictions and functional annotations.Nucleic acids research · 2026Article
- Saccharomyces cerevisiae as a model for mammalian diseases.FEMS yeast research · 2026Review
2 more citing papers are in PubMed but not listed here.
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12 authors.
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Abstract
In this update paper, we present the latest developments in the OMA browser knowledgebase, which aims to provide high-quality orthology inferences and facilitate the study of gene families, genomes and their evolution. First, we discuss the addition of new species in the database, particularly an expanded representation of prokaryotic species. The OMA browser now offers Ancestral Genome pages and an Ancestral Gene Order viewer, allowing users to explore the evolutionary history and gene content of ancestral genomes. We also introduce a revamped Local Synteny Viewer to compare genomic neighborhoods across both extant and ancestral genomes. Hierarchical Orthologous Groups (HOGs) are now annotated with Gene Ontology annotations, and users can easily perform extant or ancestral GO enrichments. Finally, we recap new tools in the OMA Ecosystem, including OMAmer for proteome mapping, OMArk for proteome quality assessment, OMAMO for model organism selection and Read2Tree for phylogenetic species tree construction from reads. These new features provide exciting opportunities for orthology analysis and comparative genomics. OMA is accessible at https://omabrowser.org.
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