PATRIC, the bacterial bioinformatics database and analysis resource

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. genomics, 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.

Subspecies in the global human gut microbiome

“…For example, we found significant differences in adhesion genes in two of four E. coli subspecies (MGSS3 and MGSS4), suggesting higher virulence potential (Lee et al , 2010). Using reference genomes and pathogenicity annotations from the PATRIC database (Wattam et al , 2014), we noted that these two subspecies were significantly enriched in isolates that caused diseases in the human host. These findings are in line with results on the corresponding phylogroups D and B2 (MGSS3 and MGSS4, respectively), which have been associated with extraintestinal infections in humans (Chakraborty et al , 2015).…”

Reconstitution of a Mycobacterium tuberculosis proteostasis network highlights essential cofactor interactions with chaperone DnaK

“…Based on analysis of >500 reported Mtb transcriptomic experiments, the most highly correlated gene for coexpression with clpB is Rv0251c, which encodes the annotated sHsp protein Hsp20 (56). We purified Mtb Hsp20 (SI Appendix, Fig.…”

Big Data in Bioinformatics

“…Большая часть из них является коммерческими продуктами, среди них наиболее известными и широко используемыми являются BaseSpace (Illumina, Inc.) [13], CLCBio [14], Lasergene (DNASTAR, Inc.) [15], Geneious [16]. Среди свободных и гибридных (частично коммерческих, частично свободных) популярными являются программные комплексы Galaxy [17,18], Globus Genomics [19], PATRIC [20], UGENE [21,22]. Они обладают широчайшими возможностями, большинство из этих программных пакетов могут быть установлены на локальный компьютер или сервер, они работают под разными операционными системами.…”