Assemble and Annotate Your Genome Sequences

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 September Release features over 4500 New Genomes, Literature Feferences, and Assembly Service Enhancements

New Genomes In this release, we have added 4653 new genomes, including replacement of 3200 Streptococcus genomes which had issues with the sequence data. This update brings the total number of genomes in PATRIC to over 79,000. The full list of available bacterial genomes can be accessed from the Genomes Tab for all bacteria, and from […]

PATRIC/RAST Workshop, November 9-11, 2016

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 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 […]

First U.S. Case of E. coli Resistant to Colistin

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 […]

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. […]