PATRIC November Release features over 9000 New Genomes, Host Genomes and Annotations, Essential Gene Predictions, Command Line Interface, RNA-Seq Service Enhancements and Other Updates.¶
New Genomes
In this release, PATRIC has added 9,136 new genomes, bringing the total number of genomes in PATRIC to over 89,000. Total 174 genomes, which were of low quality or obsolete, were deleted from PATRIC. In addition, names of 1,633 genomes were revised to include strain names to make them more informative. The full list of available bacterial genomes can be accessed from the Genomes Tab for all bacteria. on the old Production site and Genomes tab for all bacteria on the Beta website.
Protein Family and Annotation Updates
This release features complete functional re-annotation of all public genomes in PATRIC. The functional re-annotation of the genomes is carried out to propagate recent annotation changes made by PATRIC curators and to incorporate latest knowledge from the literature. During re-annotation process, the structural annotations (i.e. genomic features, gene locations, and their sequences) remain unchanged. However, all protein-coding genes (CDS) are run again through the latest annotation pipeline to reassign their functions. Changes in function may also lead to corresponding changes in the pathway assignments. The PATRIC genus-specific (PLFams) and cross-genera (PGFams) families have also been updated to reflect recent changes in the protein annotations. The protein family identifiers were preserved when the composition of the new families were mostly the same as that of old families.
Host Genomes and Annotations
PATRIC now has a set of representative host genomes in PATRIC, with annotations. These include Homo sapiens (human), Mus musculus (mouse), Macaca mulatta (Rhesus macaque monkey), Rattus norvegicus (rat), Sus scrofa (pig), Mustela putorius furo (ferret), Danio rerio (zebrafish), Gallus gallus (chicken), Drosophila melanogaster (fruit fly), and Caenorhabditis elegans (roundworm). These genomes are available in PATRIC as an option in the Organisms menu on the Beta website.
AMR Gene Annotations
With this release, PATRIC provides additional AMR gene annotations, which are propagated from set of high quality AMR genes manually curated by the PATRIC Team. These curated AMR genes correspond to 25 AMR subsystems, covering 227 unique AMR functional roles. Additional information is available here. The curated AMR gene functions have been consistently projected to more than 1.6M genes from >71,000 public bacterial genomes currently available in PATRIC. Projected AMR gene annotations are available under the Specialty Genes Tab on the website, with filters Property=Antibiotic Resistance and Source=PATRIC on the Beta website.
AMR Classifier Enhancements:
PATRIC has increased the set of AdaBoost-based machine learning AMR classifiers that are currently available in the PATRIC Genome Annotation Service by using new genomes and associated AMR resistance data. The preexisting set of classifiers have also been updated. This is an ongoing enhancement process as we bring in additional genomes into PATRIC that have AMR resistance data. The PATRIC Genome Annotation Service is available as an option in the Services menu.
Essential Gene Predictions
PATRIC now provides predicted of essential genes for 7923 Reference and Representative genomes. These essential genes were predicted using flux-balance analysis (FBA) wherein a genome-scale metabolic model is used to predict the growth conditions for an organism by simulating the simultaneous production of all the small molecule building blocks of biomass (e.g. amino acids, cofactors, nucleotides) from compounds available in the growth media (e.g. sugar, vitamins, amino acids). Additional information about this process is available from http://www.nature.com/nbt/journal/v28/n3/abs/nbt.1614.html. The essential gene predictions are available at PATRIC under the Specialty Genes Tab on the website, with filters Property=Essential Gene and Source=PATRIC on the Beta website.
Command Line and Application Programming Interfaces (CLI and API)
The initial version of the PATRIC CLI/API is now available. It allows users to programmatically batch upload data to their PATRIC workspace, invoke services (e.g., Assembly, Annotation), and download the results. The CLI/API can be downloaded as a dmg from https://github.com/PATRIC3/PATRIC-distribution/releases.
RNA-Seq Analysis Service Enhancements:
The PATRIC RNA-Seq Service is now enhanced to support RNA-Seq data using the host genomes that we currently have in PATRIC (human, mouse, monkey, rat, pig, ferret, zebrafish, chicken, fruit fly, and roundworm). The PATRIC RNA-Seq Analysis Service is available as an option in the Services menu.