PATRIC September 2013 Release Highlights Multiple Analysis Tool Enhancements, New Tutorials Page, and New Genomic and Transcriptomic Data

Website Updates

New Pathogen Interaction Gateway (PIG) for Protein-Protein Interactions

The Pathogen Interaction Gateway (PIG) provides access to inter- and intra-species protein-protein interaction (PPI) data for easy download or visualization.  PIG is available currently as a Web application on both the Pathogen Portal (bacteria, viruses, eukaryotic pathogens, hosts, and vectors) and PATRIC (bacteria and hosts) websites.  Original PPI data are periodically downloaded from public databases that include experimental data (predicted interactions are not included in PIG), and are filtered for taxa of interest, de-duplicated, and stored in local databases.  PIG allows users to select custom sets of PPIs by taxon or keyword combinations, and visualize the results in a coordinated interface that includes a sortable list and interactive PPI node-edge graphs.  Multiple taxa can be visualized simultaneously, enabling the detection of deeper interaction motifs such as host proteins targeted by multiple pathogens, or multiple classes of pathogen (bacterial, viral, eukaryotic), as well as guilt-by-association clues to the function of unknown or hypothetical proteins. 

Genome Browser Enhancements, Featuring New Colors and the Ability to Upload Your Own Data

In this release, we have incorporated the latest version of JBrowse, which provides enhanced interactivity and searching/filtering mechanisms.  The browser now displays genomic features using a new color scheme.  Different genomic feature types annotated by the same source (such as PATRIC, RefSeq, and Legacy BRC) are now grouped as a single track, using different shades of the same color to represent different feature types.  Now, users can also upload their own annotations or gene lists as GFF3 files and view them as tracks on the genome browser.  In addition, users can also upload and view their RNA-Seq, ChiP-Seq, or SNP data as tracks in the genome browser using BigWig or BAM file formats. The latest genome browser for Mycobacterium tuberculosis H37Rv can be viewed here.

Enhanced Compare Region Viewer

The Compare Region Viewer now uses the latest version of JBrowse and a new, more vibrant color scheme.  In addition, genomes displayed in the Compare Region Viewer can be filtered and sorted based on key genome metadata attributes, such as isolation country, host, disease, collection date, and completion date.  Here is an example of the Compare Region Viewer for Rv2429 gene from the Mycobacterium tuberculosis H37Rv genome.

New Transcriptomics Data Search and Display

Improvements to transcriptomics data related functionality include ability to search for transcriptomics experiments using Global Search and a new Landing Page for transcriptomics experiments, showing available metadata and curated comparisons for a single experiment.  Here is an example of the transcriptomics experiment page for the latest Burkholderia pseudomallei dataset, GSE43205, added to PATRIC.

Performance Improvements to Protein Family Sorter and Transcriptomics Gene List

The performance of the Protein Family Sorter and Transcriptomics Gene List pages have been improved to make them load faster and compare larger numbers of genomes and transcriptomics experiments, respectively.

New Tools and Tutorial Landing Pages

Two new help pages have been developed:  The Tutorials Landing Page features all available video tutorials, workflows, and step-by-step PDF tutorials showcasing how to use PATRIC data and analysis tools.  The Tools Landing Page provides descriptive summaries and links to all the tools available on PATRIC.

New Genomes and Annotations

In the September 2013 data release, 2911 new genomes have been added to PATRIC, 2887 new genomes have been annotated using RAST, 16 genomes have been updated and 2 genomes have been deleted.

A summary of the genomes available on the PATRIC website through September, 2013 is provided in the table below:

PATRIC

RefSeq

Number of genomes

11787

8964

Number of Complete genomes

2260

2204

Number of WGS genomes

9523

6361

Number of Plasmid only genomes

4

399

Featured: 42 New Brucella Genomes and 270 new Mycobacterium bovis Genomes from USDA

This data release features 42 new Brucella genomes (in addition to 106 genomes released in May) and 270 new Mycobacterium bovis genomes that are available exclusively at PATRIC. These genomes were sequenced by USDA and, subsequently, assembled and annotated by PATRIC using RAST.

Genome Metadata

In addition to manual curation of metadata for new genomes, we have also incorporated additional metadata for 712 genomes using metadata we received from NIAID-funded Genome Sequencing Centers.

New Transcriptomics Datasets

In the September data release, 20 new GEO experiments have been curated and incorporated into PATRIC.  Below is the summary of the new experiments and curated comparisons added to PATRIC since June 2013.

Organisms Experiments Comparisons
Bdellovibrio

1

1

Burkholderia

1

82

Desulfovibrio

2

9

Fusobacterium

1

3

Myxococcus

1

75

Pasteurella

2

103

Pseudomonas

13

79

Rhodobacter

1

8

Rhodopseudomonas

1

6

Zymomonas

1

4