PATRIC, the bacterial bioinformatics database and analysis resource

TLDR

PATRIC is an all‑bacterial Bioinformatics Resource Center that aggregates genomics, transcriptomics, protein–protein interactions, 3‑D structures, and sequence‑typing data from over 10,000 genomes, providing researchers with integrated metadata and analysis tools. This manuscript reports updates to PATRIC since its 2007 NAR Database Issue release. PATRIC annotates all genomes with RAST, offers genome‑ and gene‑level summaries, a private workspace, and a suite of free comparative genomic and transcriptomic tools that integrate disease and PPI data.

Abstract

The Pathosystems Resource Integration Center (PATRIC) is the all-bacterial Bioinformatics Resource Center (BRC) (http://www.patricbrc.org). A joint effort by two of the original National Institute of Allergy and Infectious Diseases-funded BRCs, PATRIC provides researchers with an online resource that stores and integrates a variety of data types [e.g. geomics, transcriptomics, protein–protein interactions (PPIs), three-dimensional protein structures and sequence typing data] and associated metadata. Datatypes are summarized for individual genomes and across taxonomic levels. All genomes in PATRIC, currently more than 10 000, are consistently annotated using RAST, the Rapid Annotations using Subsystems Technology. Summaries of different data types are also provided for individual genes, where comparisons of different annotations are available, and also include available transcriptomic data. PATRIC provides a variety of ways for researchers to find data of interest and a private workspace where they can store both genomic and gene associations, and their own private data. Both private and public data can be analyzed together using a suite of tools to perform comparative genomic or transcriptomic analysis. PATRIC also includes integrated information related to disease and PPIs. All the data and integrated analysis and visualization tools are freely available. This manuscript describes updates to the PATRIC since its initial report in the 2007 NAR Database Issue.