PGAT is designed to facilitate comparative analysis of closely related bacterial genomes under study. A novel algorithm was developed to identify the genes present in a set of genomes, and to map orthologs between the genomes. A web interface facilitates the exploration and analysis of the genomic similarities and differences between the various bacterial strains based on these ortholog mappings.

Genome Search and Browsing

PGAT search tools enable identification of genes based on keyword, gene id (gene name, locus tag or genbank accession number), or functional category. Sets of genes returned by user searches can be saved for use in PGAT's comparative analysis features. Researchers may explore genes of interest and their neighboring genome features through the PGAT's genome visualization tools and gene detail pages.

Comparative Analysis

The following list highlights a few of the comparative analysis features built into PGAT:

Explore PGAT Features

Curated Annotation

Please email us suggestions and corrections for annotation. Annotators and curators (login required) can make modifications to annotation, including gene name and description, gene chromosomal positions, and ortholog mappings. Bioinformatics predictions, such as COG, PFAM, PSort, and BLAST results are included in the tool for each reference gene to faciliate annotation. Because PGAT is web-based, it enables multiple researchers in remote locations to easily access the tool and collaborate on annotation tasks.

PGAT Training Workshops

We periodically offer training workshops to introduce new users to PGAT and to demonstrate advanced features of the tool. Researchers are invited to bring their own laptops and work to the sessions and the PGAT developers will be available to answer questions. The date of the next workshop has not been determined. Please email nwrce_tools@uw.edu if you are interested or want more information.

Funding

Funding for PGAT is provided by National Institutes of Health (NIH) and National Institute of Allergy and Infectious Diseases (NIAID) grants to the Northwest Regional Center of Excellence for Biodefense & Emerging Infectious Diseases Research (NWRCE) and Enterics Research Investigational Network Cooperative Research Center (ERIN).