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. For each sample, the service computes the variations against the reference and presents a detailed list of SNPs, MNPs, insertions and deletions with confidence scores and effects such as “synonymous mutation” and “frameshift”. High confidence variations are downloadable in the standard VCF format augmented by SNP annotation. A summary table illustrating how the variations are shared across the samples is also available. The PATRIC Variation Service can be accessed at https://www.patricbrc.org/app/Variation.

Annotation Service Enhancements

The PATRIC Genome Annotation Service now includes an AMR classifier module built into RASTtk that performs species-specific AMR phenotype and genomic feature prediction. This classifier was built using PATRIC’s collection of genomes, binned by AMR phenotype along with metadata including minimum inhibitory concentrations (MICs). From this, we custom built AdaBoost (adaptive boosting) machine learning classifiers for identifying carbapenem resistance in Acinetobacter baumannii, methicillin resistance in Staphylococcus aureus, and beta-lactam and co-trimoxazole resistance in Streptococcus pneumonia. We also did this for isoniazid, kanamycin, ofloxacin, rifampicin, and streptomycin resistance in Mycobacterium tuberculosis. A corresponding manuscript has been submitted. The PATRIC Genome Annotation Service can be accessed at https://www.patricbrc.org/app/Annotation.

Proteome Comparison Service Enhancements

PATRIC’s Proteome Comparison Service now allows users to select a public or a private genome in PATRIC as a reference genome, as well as a user-supplied FASTA file or saved feature group as the reference. The service now also supports selection of multiple FASTA files and/or feature groups for comparison. The PATRIC Proteome Comparison Service can be accessed at https://www.patricbrc.org/app/SeqComparison.

Curated Antimicrobial Resistance (AMR) Genes

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. Curation thus far has focused on encoding the following mechanisms of drug resistance: outer membrane porins, multidrug efflux mechanisms, and capsular and extracellular polysaccharides. To date, we have encoded 25 subsystems covering 265 unique functional roles (protein families). Additional information and curated data are available here.

Changes to the FTP Site

We have completed reorganization and updating of the PATRIC FTP site. It now contains downloadable updated FTP files for all PATRIC protein-protein interaction data, available from ftp://ftp.patricbrc.org/patric2/ppi/.

New Genomes, Annotations, and Other Data

In this release, 9280 new genomes have been added to PATRIC, bringing the total to over 67,000. Approximately 4600 of these genomes are from the Sanger Center and are part of large-scale sequencing projects. This release also included 173 Staphylococcus and Streptococcus genomes with AMR and clinical metadata from a PATRIC collaboration. We have also updated the list of reference and representative genomes based on the latest NCBI and Uniprot Reference genome sets. The genomes labeled as ref/rep at PATRIC before, are still labeled as such. Also included are additional curated AMR metadata from NIAID Genomics Centers for Infectious Diseases, and are available as part of the master AMR metadata spreadsheet on the FTP site.

We have added additional project descriptions and experimental data from two of the NIAID Functional Genomics Centers: The Chicago Center for Functional Annotation (CCFA) and Genes Unknown in Acinetobacter baumannii (GUNK). These are available from the respective pages in PATRIC: CCFA and GUNK.  We have also added project descriptions and data from the Omics4TB Disease Progression, a NIAID Systems Biology Center, available from the Omics4TB page in PATRIC.