New Services and Data in PATRIC

PATRIC has added several new services and data resources in the July 2017 Release: Phylogenetic Tree Builder constructs custom phylogenetic trees using conserved protein sequences. Tn-Seq Analysis aligns reads and measures essentiality of Tn-seq data using the TRANSIT software. Similar Genome Finder finds the closest related genomes to selected genome or FASTA file using MInHash. Compare Region Viewer displays […]

PATRIC/RAST Tutorial Workshop, July 26-28, 2016

The PATRIC/RAST teams will be offering a tutorial on July 26-28, 2016 at Argonne National Laboratory in the suburbs of Chicago, IL. The workshop will run for three days with the third day optional and devoted solely to participants working on their own problems with help from the PATRIC/RAST team members. The tutorial will show […]

PATRIC / RAST Tutorial Workshop Agenda

by patricwpadmin

Dates: July 26 – 28, 2016 Location: Argonne National Laboratory, Argonne, IL Agenda: Tuesday, July 26 9am                PATRIC Introduction and registration 10am              Genome Assembly 11am              Genome Annotation and exploration 12pm              Lunch 1pm                SNP pipeline 2pm                Proteome Comparison 3pm                Questions and adjournment Wednesday, July 27 9am                Comparative Genomics 12pm              Lunch 1pm                RNA-Seq 2pm                Upload […]

PATRIC March 2016 Release Features a New Variation Analysis Service, Service Enhancements, New AMR and other Data, and over 9000 New Genomes

NOTE: You must have a PATRIC user account and be logged in to use the services and workspace. Variation Analysis Service The new Variation Service can be used to identify and annotate sequence variations. The service enables users to upload one or multiple short read samples and compare them to a closely related reference genome. […]

Omics4TB TFOE Expression Experiments

by patricwpadmin

Mycobacterium tuberculosis senses and responds to the shifting and hostile landscape of the host. To characterize the underlying intertwined gene regulatory network governed by approximately 200 transcription factors of M. tuberculosis, we have assayed the global transcriptional consequences of overexpressing each transcription factor from an inducible promoter. We cloned and overexpressed 206 transcription factors in […]

Omics4TB ChIP-Seq Experiments

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 Antimicrobial Resistance (AMR) Gene Curation

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 Workshop at ASM Microbes 2016 in Boston

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 […]

GUNK Experiment 1

by patricwpadmin

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 […]

PATRIC January 2016 Release Features Over 2400 New Genomes

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 […]

FLUTE Experiment 2

by patricwpadmin

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 […]