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 of available bacterial genomes can be accessed from the Genomes Tab for all bacteria, and from the Genomes Data Landing Page.
AMR Panel Data: This release also includes AMR panel data curated from publications for 5442 genomes. The AMR panel data is displayed on the corresponding genome overview pages. All available AMR panel data can be downloaded from here. Additional manual curatuion was performed to clean up all AMR panel data collected so far for consistency and accuracy.
AMR Gene Annotations: 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. In addition, we thee curated AMR gene functions have been consistently projected to more than 1.6M genes from all public bacterial genomes currently available in PATRIC. Projected AMR gene annotations are available here.
New Alpha Version of Website: We have also released an Alpha Version of the new PATRIC website design that is built on a new software platform to enhance flexibility and efficiency in software development. It also streamlines workflows and makes the website navigation and interactions more consistent throughout.
Note: The Alpha version is intended for testing and evaluation only. If you would like to participate in testing the Alpha system, please send an email to email@example.com and include the phrase “Alpha Testing” in the title of the email.