Genome properties in 2019: a new companion database to InterPro for the inference of complete functional attributes
Open accessAbstract
Automatic annotation of protein function is routinely applied to newly sequenced genomes. While this provides a fine-grained view of an organism's functional protein repertoire, proteins, more commonly function in a coordinated manner, such as in pathways or multimeric complexes. Genome Properties (GPs) define such functional entities as a series of steps, originally described by either TIGRFAMs or Pfam entries. To increase the scope of coverage, we have migrated GPs to function as a companion resource utilizing InterPro entries. Having introduced GPs-specific versioned releases, we provide software and data via a GitHub repository, and have developed a new web interface to GPs (available at https://www.ebi.ac.uk/interpro/genomeproperties). In addition to exploring each of the 1286 GPs, the website contains GPs pre-calculated for a representative set of proteomes; these results can be used to profile GPs phylogenetically via an interactive viewer. Users can upload novel data to the viewer for comparison with the pre-calculated results. Over the last year, we have added ∼700 new GPs, increasing the coverage of eukaryotic systems, as well as increasing general coverage through automatic generation of GPs from related resources. All data are freely available via the website and the GitHub repository.
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MGnify's latest update v5.0, released September 2019, extends analyses further, substantially increasing the scope of functional annotations through the addition of KEGG orthologue predictions for reads and assembled contigs, and KEGG pathways and Genome Properties annotations for assembled contigs.
“The latest update (v5.0), released September 2019, extends the analyses further, substantially increasing the scope of functional annotations through the addition of KEGG (23) orthologue predictions for reads and assembled contigs, and KEGG pathways and Genome Properties (24) annotations for assembled contigs.”
From MGnify: the microbiome analysis resource in 2020 (2019) · cites this paper as [24]
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References 28 · Cited by 36
- Authors
- Richardson, L. J., Rawlings, N. D., Salazar, G. A., Almeida, A., Haft, D. R., Ducq, G., Sutton, G. G., & Finn, R. D.
- Affiliations
- European Bioinformatics Institute (GB)
- J. Craig Venter Institute (US)
- Corresponding author
- Finn, Robert D
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2018-10-26
- Volume
- 47
- Issue
- D1
- Pages
- D564-D572
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC6323913
- OpenAlex
- W2898548494
- Cited by
- 36
- References
- 28
- Citations by year
- 2026: 1 · 2025: 6 · 2024: 2 · 2023: 4 · 2022: 5 · 2021: 6 · 2020: 5 · 2019: 6 · 2018: 1
- FWCI
- 2.22
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Nucleic Acids Research (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Funders
- National Science Foundation (1458808)
- Biotechnology and Biological Sciences Research Council (BB/N00521X/1)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Machine Learning in Bioinformatics
- Keywords
- InterPro, protein annotation, protein pathways, Pfam, phylogenetic profiling, eukaryotic proteomes, online databases
- MeSH terms
- Proteins, Genome, Proteome, Databases, Protein, Multiprotein Complexes, Metabolic Networks and Pathways, Genome, Microbial
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