The OMA orthology database in 2018: Retrieving evolutionary relationships among all domains of life through richer web and programmatic interfaces
| Autor: | Altenhoff, Adrian M, Glover, Natasha M, Train, Clément-Marie, Kaleb, Klara, Warwick Vesztrocy, Alex, Dylus, David, de Farias, Tarcisio M, Zile, Karina, Stevenson, Charles, Long, Jiao, Redestig, Henning, Gonnet, Gaston H, Dessimoz, Christophe |
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| Jazyk: | angličtina |
| Rok vydání: | 2018 |
| Předmět: |
Internet
Genome Bacteria Fungi Computational Biology Proteins Molecular Sequence Annotation Plants Web Browser Archaea Biological Evolution Synteny Gene Ontology Protein Domains Algorithms Animals Archaea/classification Archaea/genetics Archaea/metabolism Bacteria/classification Bacteria/genetics Bacteria/metabolism Computational Biology/methods Databases Genetic Fungi/classification Fungi/genetics Fungi/metabolism Humans Phylogeny Plants/classification Plants/genetics Plants/metabolism Proteins/chemistry Proteins/genetics Proteins/metabolism Database Issue |
| Zdroj: | Nucleic Acids Research, 46 (D1) Nucleic acids research, vol. 46, no. D1, pp. D477-D485 Nucleic Acids Research |
| ISSN: | 1362-4962 |
| Popis: | 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. ISSN:1362-4962 ISSN:0301-5610 |
| Databáze: | OpenAIRE |
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