The next PATRIC/RAST workshop will be held Wednesday, November 9, 2016 – Friday, November 11, 2016 at Argonne National Laboratory. We will post further details once they become available.
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 July 2016 Release Features Over 7600 New Genomes and AMR Panel Data for Approximately 5400 Genomes. PATRIC Also Releases Alpha Version of New Website Design.
New genomes: In this release, we have added 7,683 new genomes, bringing the total number of genomes in PATRIC to over 77,000. 5,483 of the new genomes are from published AMR studies and were assembled from the reads available in NCBI SRA database. The remaining 2200 genomes were added from NCBI GenBank. The full list […]
PATRIC May 2016 Release Features Over 700 New Genomes and AMR Panel Data for Approximately 1800 Genomes
In this release, we have added 748 new genomes from NCBI GenBank, bringing the total number of genomes in PATRIC to over 70,000. The full list of available bacterial genomes can be accessed from the Genomes Tab for all bacteria, and from the Genomes Data Landing Page. This release includes a special genome, corresponding to […]
The assembled genome of Colistin-resistant E. coli MRSN 388634 is now available in PATRIC here. Sequence reads for MRSN388634 have been deposited in the NCBI Short Read Archive by researchers at the Walter Reed Army Institute of Research and Walter Reed National Military Medical Center under Accession number SRP075674. The authors report the presence of […]
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 […]
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. […]
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 […]
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 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 […]