Comparative genomic studies often include an analysis of sequence homologies between the genomes under study. An additional analysis of the genomic neighborhood surrounding the homologs, however, may also suggest interesting gene characteristics or potential evolutionary mechanisms. For example, conserved gene order between genomes might provide support for gene orthology or help identify a potential functional gene cluster.
We have developed the Prokaryotic Sequence homology Analysis Tool (PSAT) to provide researchers an easy and efficient method for investigating homologs among multiple genomes and examining their genomic neighborhoods. PSAT is a web-based tool developed completely using open source software. It uses a PostgreSQL database backend, Perl CGI scripts to dynamically generate the web interface, and the ImageMagick graphics package for generating images of genes within genomic neighborhoods to compare.
To begin using the PSAT web server, you can begin from the PSAT querying page which can always be accessed from the Explore Homologies menu item at the top of each page.
The querying page is a web interface for specifying query constraints for a multiple genome homolog analysis. You may select a single reference genome from a list of available reference genomes and any number of available comparison genomes. Query options include searching for a specific gene in the reference genome, retrieving a list of homologs for a complete genome, comparing subsets of genomes based on homologies found against the reference, or comparing genomes based on homology statistics. You may also specify BLAST hit score thresholds to narrow the returned list of homologs in the results. For more information about these querying options and using the tool features for exploring the results, see the PSAT User's Manual.
PSAT source code is freely available so you can setup a local installation of the analysis tool for studying genomes that are not available on our PSAT web server, such as unpublished genomes. Visit the Download page to get the source code and instructions for installation.
If you use PSAT for your research, please cite the following publication:
Fong C, Rohmer L, Radey M, Wasnick M, Brittnacher MJ. PSAT: A web tool to compare genomic neighborhoods of multiple prokaryotic genomes. BMC Bioinformatics. 2008 Mar 26;9(1):170
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