OMA orthology in 2024: improved prokaryote coverage, ancestral and extant GO enrichment, a revamped synteny viewer and more in the OMA Ecosystem.

Details

Serval ID
serval:BIB_B96DA0D62CDE
Type
Article: article from journal or magazin.
Collection
Publications
Institution
Title
OMA orthology in 2024: improved prokaryote coverage, ancestral and extant GO enrichment, a revamped synteny viewer and more in the OMA Ecosystem.
Journal
Nucleic acids research
Author(s)
Altenhoff A.M., Warwick Vesztrocy A., Bernard C., Train C.M., Nicheperovich A., Prieto Baños S., Julca I., Moi D., Nevers Y., Majidian S., Dessimoz C., Glover N.M.
ISSN
1362-4962 (Electronic)
ISSN-L
0305-1048
Publication state
Published
Issued date
05/01/2024
Peer-reviewed
Oui
Volume
52
Number
D1
Pages
D513-D521
Language
english
Notes
Publication types: Journal Article
Publication Status: ppublish
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.
Keywords
Ecosystem, Genome/genetics, Phylogeny, Proteome, Synteny, Internet, Databases, Genetic, Gene Order/genetics
Pubmed
Web of science
Open Access
Yes
Create date
16/11/2023 14:58
Last modification date
16/01/2024 8:12
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