The OMA orthology database in 2018: retrieving evolutionary relationships among all domains of life through richer web and programmatic interfaces.

Details

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State: Public
Version: Final published version
Serval ID
serval:BIB_FC0F04688D1D
Type
Article: article from journal or magazin.
Collection
Publications
Institution
Title
The OMA orthology database in 2018: retrieving evolutionary relationships among all domains of life through richer web and programmatic interfaces.
Journal
Nucleic acids research
Author(s)
Altenhoff A.M., Glover N.M., Train C.M., Kaleb K., Warwick Vesztrocy A., Dylus D., de Farias T.M., Zile K., Stevenson C., Long J., Redestig H., Gonnet G.H., Dessimoz C.
ISSN
1362-4962 (Electronic)
ISSN-L
0305-1048
Publication state
Published
Issued date
04/01/2018
Peer-reviewed
Oui
Volume
46
Number
D1
Pages
D477-D485
Language
english
Notes
Publication types: Journal Article ; Research Support, Non-U.S. Gov't
Publication Status: ppublish
Abstract
The Orthologous Matrix (OMA) is a leading resource to relate genes across many species from all of life. In this update paper, we review the recent algorithmic improvements in the OMA pipeline, describe increases in species coverage (particularly in plants and early-branching eukaryotes) and introduce several new features in the OMA web browser. Notable improvements include: (i) a scalable, interactive viewer for hierarchical orthologous groups; (ii) protein domain annotations and domain-based links between orthologous groups; (iii) functionality to retrieve phylogenetic marker genes for a subset of species of interest; (iv) a new synteny dot plot viewer; and (v) an overhaul of the programmatic access (REST API and semantic web), which will facilitate incorporation of OMA analyses in computational pipelines and integration with other bioinformatic resources. OMA can be freely accessed at https://omabrowser.org.
Keywords
Algorithms, Animals, Archaea/classification, Archaea/genetics, Archaea/metabolism, Bacteria/classification, Bacteria/genetics, Bacteria/metabolism, Biological Evolution, Computational Biology/methods, Databases, Genetic, Fungi/classification, Fungi/genetics, Fungi/metabolism, Gene Ontology, Genome, Humans, Internet, Molecular Sequence Annotation, Phylogeny, Plants/classification, Plants/genetics, Plants/metabolism, Protein Domains, Proteins/chemistry, Proteins/genetics, Proteins/metabolism, Synteny, Web Browser
Pubmed
Web of science
Open Access
Yes
Create date
15/11/2017 10:25
Last modification date
17/01/2020 9:51
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