ArticleNucleic acids research2013
OrthoDB: a hierarchical catalog of animal, fungal and bacterial orthologs.
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 205 papers.
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205 citing papers in PubMed.
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- Orthoptera-specific target enrichment (OR-TE) probes resolve relationships over broad phylogenetic scales.Scientific reports · 2024Article
- A taxon-rich and genome-scale phylogeny of Opisthokonta.PLoS biology · 2024Article
- Solving genomic puzzles: computational methods for metagenomic binning.Briefings in bioinformatics · 2024Review
- Comparative Genomics and the Salivary Transcriptome of the Redbanded Stink Bug Shed Light on Its High Damage Potential to Soybean.Genome biology and evolution · 2024Article
- Functional exploration of copy number alterations in a Drosophila model of triple-negative breast cancer.Disease models & mechanisms · 2024Article
- A novel approach to exploring the dark genome and its application to mapping of the vertebrate virus fossil record.Genome biology · 2024Article
145 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The concept of orthology provides a foundation for formulating hypotheses on gene and genome evolution, and thus forms the cornerstone of comparative genomics, phylogenomics and metagenomics. We present the update of OrthoDB-the hierarchical catalog of orthologs (http://www.orthodb.org). From its conception, OrthoDB promoted delineation of orthologs at varying resolution by explicitly referring to the hierarchy of species radiations, now also adopted by other resources. The current release provides comprehensive coverage of animals and fungi representing 252 eukaryotic species, and is now extended to prokaryotes with the inclusion of 1115 bacteria. Functional annotations of orthologous groups are provided through mapping to InterPro, GO, OMIM and model organism phenotypes, with cross-references to major resources including UniProt, NCBI and FlyBase. Uniquely, OrthoDB provides computed evolutionary traits of orthologs, such as gene duplicability and loss profiles, divergence rates, sibling groups, and now extended with exon-intron architectures, syntenic orthologs and parent-child trees. The interactive web interface allows navigation along the species phylogenies, complex queries with various identifiers, annotation keywords and phrases, as well as with gene copy-number profiles and sequence homology searches. With the explosive growth of available data, OrthoDB also provides mapping of newly sequenced genomes and transcriptomes to the current orthologous groups.
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