Escobase

DOI

Compiling the Escobase (EScherichia COli dataBASE) was part of Lucile Martin's Internship for her MSc-1 at the University of Clermont-Auvergne, who PS supervised from May-August 2023.

The E. coli genomes were downloaded or assembled with SPADES (when only reads were present), and after examination of the metadata to select only the genomes of isolates from cattle, the Escobase was put together. We compared the predicted ORFs (identified with Prodigal) of all genomes to the virulence factor database (VFdb), the ResFinder AMR database, and a custom-made database using genes which have been shown to contribute to bacterial acid resistance (AcR_AA_nr_latest30Dec2024.faa ).

Identifier
DOI https://doi.org/10.57745/RGIZYC
Related Identifier IsCitedBy https://doi.org/10.1089/fpd.2021.0082
Metadata Access https://entrepot.recherche.data.gouv.fr/oai?verb=GetRecord&metadataPrefix=oai_datacite&identifier=doi:10.57745/RGIZYC
Provenance
Creator Sapountzis, Panagiotis ORCID logo; Martin, Lucile ORCID logo; Ruiz, Philippe ORCID logo; Leroy, Sabine
Publisher Recherche Data Gouv
Contributor Sapountzis, Panagiotis; UMR 454 Microbiologie, Environnement Digestif, Santé; Entrepôt-Catalogue Recherche Data Gouv
Publication Year 2025
Funding Reference INRAE
Rights etalab 2.0; info:eu-repo/semantics/openAccess; https://spdx.org/licenses/etalab-2.0.html
OpenAccess true
Contact Sapountzis, Panagiotis (INRAE)
Representation
Resource Type Dataset
Format application/octet-stream; text/tab-separated-values; text/comma-separated-values
Size 282043; 4821815249; 3801395; 162765; 755
Version 2.0
Discipline Agriculture, Forestry, Horticulture; Computer Science; Geosciences; Agricultural Sciences; Agriculture, Forestry, Horticulture, Aquaculture; Agriculture, Forestry, Horticulture, Aquaculture and Veterinary Medicine; Earth and Environmental Science; Environmental Research; Life Sciences; Natural Sciences