PATRIC July 2014 Release Features New Circular Genome Viewer, Group Explorer, Integration of Protein-Protein Interaction Data, and New Genomic and Transcriptomic Data
New Circular Genome Viewer
This website release features a new Circular Genome Viewer, implemented using Circos, which is one of the most popular and highly cited tool for generating publication quality circular genome maps. The viewer is accessible from any genome-level page on the PATRIC website, under the “Circular Viewer” tab. By default, the viewer displays chromosomes/plasmids/contigs; genes on forward and reverse strands; RNAs; other miscellaneous features; average GC content and GC skew plots; as separate tracks. Users can add custom tracks showing genes of interest by specifying keywords. The viewer also allows users to upload their data, such as custom gene lists or genomic regions, by providing corresponding genomic locations in a simple tab delimited format. Additional quantitative values can be provided as a separate column in the data file to display gene or protein expression data as a heatmap or histogram plots. Please see an example of the Circular Genome Viewer for the genome Mycobacterium tuberculosis H37Rv.
Updated Group Explorer
Integration of Protein-Protein Interaction Data
The host-pathogen and pathogen protein-protein interaction data and viewer is now integrated throughout the PATRIC website and can be accessed at taxon, genome and gene levels, under the “Interactions” Tab.
New Genomes and Annotations
A summary of the genomes (by annotation source) available on the PATRIC website through July, 2014 is provided in the table below:
|Number of Genomes||
|Number of Complete Genomes||
|Number of WGS Genomes||
|Number of Plasmid Only Genomes||
Featured: 1522 Mycobacterium tuberculosis Genomes from NIAID TB-ARC Project
This release features the addition of 1522 new Mycobacterium tuberculosis complex genomes to PATRIC. These genomes were sequenced by Broad Institute as part of the TB Antibiotic Resistance Catalog (TB-ARC) project funded by NIAID. The overarching goal of the TB-ARC project is to create a comprehensive catalog of drug resistance conferring mutations by sequencing large numbers of geographically and phenotypically diverse Mtb strains that have been quantitatively characterized for their resistance to a broad spectrum of first and second line antibiotics.
In addition to curating metadata for new genomes, we have incorporated additional metadata provided to PATRIC by the NIAID-funded Genome Sequencing Centers for a total of 1650 Staphylococcus aureus genomes, which were sequenced as part of multiple MRSA surveillance programs.
New Transcriptomics Datasets
In the July data release, 81 new transcriptomics experiments from GEO have been curated and incorporated into PATRIC.