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.
The following list highlights a few of the comparative analysis features built into PGAT:
- Pan Genome / Core Genes : download files for genes across all genomes or genes only present in all genomes
- Synteny : compare order of genes among different strains within the genomic neighborhood of a selected gene
For a related tool exploring synteny among multiple genomes, including distant genomes, see our
Prokaryotic Sequence homology Analysis Tool (PSAT)
- Presence and Absence : retrieve tables of presence and absence of selected genes within different genomes
- Pathway Analysis : investigate genes and pseudogenes that are mapped on KEGG pathways
- SNP Analysis : generate lists of SNPs in a gene among selected genomes
- Integrated BLAST and DIALIGN queries : quickly retrieve sequence homologies or multiple sequence alignments using alignment tools integrated directly into the PGAT web interface
Explore PGAT Features
- Demo tool for Acinetobacter baumannii :
In addition to exploring PGAT's genome browsing, search and comparison tools, you may make annotation changes to explore the genome curation features.
- Screenshots : View screenshots of some of PGAT's features
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 firstname.lastname@example.org if you are interested or want more information.
Support for PGAT comes from grants from the National Institutes of Health for the Cystic Fibrosis Research and Translation Center
, from the Cystic Fibrosis Foundation for the Cystic Fibrosis Research Development Program
and from the NIH National Institute of Allergy and Infectious Diseases for the Functional Genomics Program