OrthoDB: a hierarchical catalog of animal, fungal and bacterial orthologs.
Details
State: Public
Version: Final published version
License: Not specified
Serval ID
serval:BIB_7EAD49D651C6
Type
Article: article from journal or magazin.
Publication sub-type
Minutes: analyse of a published work.
Collection
Publications
Institution
Title
OrthoDB: a hierarchical catalog of animal, fungal and bacterial orthologs.
Journal
Nucleic Acids Research
ISSN
1362-4962 (Electronic)
ISSN-L
0305-1048
Publication state
Published
Issued date
2013
Peer-reviewed
Oui
Volume
41
Number
Database issue
Pages
D358-65
Language
english
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.
Keywords
Animals, Cluster Analysis, Databases, Genetic, Evolution, Molecular, Genes, Genes, Bacterial, Genes, Fungal, Humans, Internet, Mice, Molecular Sequence Annotation, Phenotype, Phylogeny, Synteny
Pubmed
Web of science
Open Access
Yes
Create date
20/09/2017 11:05
Last modification date
03/01/2020 19:10