Camargo, Antonio Pedro 
ORCID: 0000-0003-3913-2484, Call, Lee ORCID: 0000-0002-2857-1337, Roux, Simon ORCID: 0000-0002-5831-5895, Nayfach, Stephen ORCID: 0000-0003-4625-4164, Huntemann, Marcel ORCID: 0000-0002-1284-3748, Palaniappan, Krishnaveni ORCID: 0000-0003-4484-7505, Ratner, Anna ORCID: 0000-0001-8877-2002, Chu, Ken ORCID: 0000-0002-9602-1433, Mukherjeep, Supratim ORCID: 0000-0002-6322-2271, Reddy, TBK ORCID: 0000-0002-0871-5567 et al (show 14 more authors)
(2024)
IMG/PR: a database of plasmids from genomes and metagenomes with rich annotations and metadata.
Nucleic acids research, 52 (D1).
D164-D173.
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IMG_PR_manuscript_AAM.pdf - Author Accepted Manuscript Download (1MB) | Preview |
Abstract
Plasmids are mobile genetic elements found in many clades of Archaea and Bacteria. They drive horizontal gene transfer, impacting ecological and evolutionary processes within microbial communities, and hold substantial importance in human health and biotechnology. To support plasmid research and provide scientists with data of an unprecedented diversity of plasmid sequences, we introduce the IMG/PR database, a new resource encompassing 699 973 plasmid sequences derived from genomes, metagenomes and metatranscriptomes. IMG/PR is the first database to provide data of plasmid that were systematically identified from diverse microbiome samples. IMG/PR plasmids are associated with rich metadata that includes geographical and ecosystem information, host taxonomy, similarity to other plasmids, functional annotation, presence of genes involved in conjugation and antibiotic resistance. The database offers diverse methods for exploring its extensive plasmid collection, enabling users to navigate plasmids through metadata-centric queries, plasmid comparisons and BLAST searches. The web interface for IMG/PR is accessible at https://img.jgi.doe.gov/pr. Plasmid metadata and sequences can be downloaded from https://genome.jgi.doe.gov/portal/IMG_PR.
| Item Type: | Article |
|---|---|
| Uncontrolled Keywords: | Humans, Plasmids, Software, Databases, Genetic, Metagenome, Microbiota, Metadata |
| Divisions: | Faculty of Health and Life Sciences Faculty of Health and Life Sciences > Institute of Infection, Veterinary and Ecological Sciences |
| Depositing User: | Symplectic Admin |
| Date Deposited: | 17 Nov 2023 08:04 |
| Last Modified: | 20 Jan 2024 01:27 |
| DOI: | 10.1093/nar/gkad964 |
| Related URLs: | |
| URI: | https://livrepository.liverpool.ac.uk/id/eprint/3176783 |
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