Mycobacterium tuberculosis (MTB) is a pathogenic bacterium responsible for 12 million active cases of tuberculosis (TB) worldwide. The complexity and critical regulatory components of MTB pathogenicity are still poorly understood despite extensive research efforts. In this study, we constructed the first systems-scale map of transcription factor (TF) binding sites and their regulatory target proteins in MTB. […]
PATRIC now provides genome assembly and annotation services. Users can bring their sequence reads, upload them into the private workspace, assembly and annotate them, and download the fully annotated genome.
PATRIC has undertaken an antimicrobial resistance (AMR) curation effort with the goal of providing PATRIC users with the ability to rapidly recognize and project known AMR related genome features to new genomes in an automated fashion and to use comparative genomics approaches for the discovery of new resistance mechanisms. Specific Aims: Catalog published AMR related […]
PATRIC will be hosting a 1-day workshop entitled, “Assemble, Annotate and Analyze Your Own Genome using PATRIC, the All Bacterial Bioinformatics Resource Center,” workshop number 013-WS, at the ASM Microbes 2016 on June 16, 2016 in Boston, Massachusetts. The workshop will cover comparative genomics, genome assembly and annotation, metabolic modeling, and transcriptomics analysis in PATRIC. The […]
Resources for Genetic and Genomic Analysis of Emerging Pathogen Acinetobacter baumannii Publication: PMC4438207 Acinetobacter baumannii is a Gram-negative bacterial pathogen notorious for causing serious nosocomial infections that resist antibiotic therapy. Research to identify factors responsible for the pathogen’s success has been limited by the resources available for genome-scale experimental studies. This report describes the development […]
In this release, we have added 2466 new genomes from NCBI GenBank, bringing the total number of genomes in PATRIC to over 57,000. This release utilizes our newly deployed continuous release process wherein we can release genomes into the database in near real-time from acquisition from GenBank and other sources. The full list of available […]
Peptidoglycan synthesis in Mycobacterium tuberculosis is organized into networks with varying drug susceptibility Publication: PMCID: PMC4620856 Peptidoglycan (PG), a complex polymer composed of saccharide chains crosslinked by short peptides, is a critical component of the bacterial cell wall. PG synthesis has been extensively studied in model organisms but remains poorly understood in mycobacteria, a genus that […]
New Genomes and Annotation System Enhancements In this release, we have added 23,052 new genomes from NCBI GenBank, bringing the total number of genomes in PATRIC to over 54,000. The full list of available bacterial genomes can be accessed from the Genomes Tab for all bacteria, and from the Genomes Data Landing Page. As part […]
Tutorial workflows for the workshop: Chicago PATRIC Flyer – Dec. 2015 (1) Creating Genome Groups Exploring your annotated genome in PATRIC Fastq download from ENA Genome Annotation in PATRIC Genome Group Assignment Protein Family Analysis- Protein Family Sorter Protein Family Analysis- Proteome Comparison Protein Family Analysis-Comparative Pathway Viewer Submitting an assembly job to PATRIC Transcriptomics […]
AMR Metadata In this release, we have added additional antimicrobial resistance phenotype related metadata for 949 genomes. The AMR panel data was primarily provided by the NIAID Genomic Centers for Infectious Diseases, which was incorporated into PATRIC after a comprehensive manual curation process. Below is the summary of the top bacterial genera with AMR metadata. […]
On August 31 – September 1, 2015, a two-day PATRIC workshop was conducted at the Houston Methodist Research Institute in Houston, Texas. There were 32 participants, which included graduate students, post docs and professors.This workshop introduced the new PATRIC services (assembly, annotation, proteome comparison, RNA-Seq and metabolic modeling) demonstrated through hands-on tutorials.