PATRIC July 2014 Release Features New Circular Genome Viewer, Group Explorer, Integration of Protein-Protein Interaction Data, and New Genomic and Transcriptomic Data

Website Updates

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 

The Group Explorer allows you to compare and contrast selected groups from within your customized Workspace using a Venn diagram-based interactive visualization.  We have re-implemented the Group Explorer Tool using the latest web technologies, SVG and JavaScript, to make it accessible from different web browsers.  In addition, the new viewer is more interactive and allows one to save the Venn diagram as an SVG or PNG image.

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

In the July 2014 data release, 6083 new genomes have been added to PATRIC, with 6056 having been annotated using RAST.  In addition, 51 genomes have been updated and 6 genomes have been deleted.

A summary of the genomes (by annotation source) available on the PATRIC website through July, 2014 is provided in the table below:

PATRIC

RefSeq

Number of Genomes

21640

16128

Number of Complete Genomes

2676

2573

Number of WGS Genomes

18959

13156

Number of Plasmid Only Genomes

5

399

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.

Genome Metadata

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.

 Organism

New Experiments

 Pseudomonas 18
 Salmonella 11
 Bacillus 7
 Streptococcus 6
 Staphylococcus 5
 Campylobacter 5
 Mycobacterium 4
 Listeria 4
 Clostridium 4
 Xanthomonas 2
 Chlamydia 2
 Xylella 1
 Vibrio 1
 Streptomyces 1
 Saccharopolyspora 1
 Rhodocuccus 1
 Escherichia 1
 Corynebacterium 1
 Brucella 1
 Bradyrhizobium 1
 Bdellovibrio 1
 Aliivibrio 1
 Actinobacillus 1