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PSAT: Prokaryotic Sequence homology Analysis Tool

Find Syntenic Regions Using PSAT

User's Manual

Browse Genes


What is PSAT?

PSAT is a web-based tool enabling researchers to quickly analyze protein sequence homologs between a reference bacterial genome and any number of other bacterial genomes published on NCBI. A major feature of PSAT is its identification of homolog clusters among the genomes under study, helping researchers to explore potential syntenic regions among these genomes. PSAT is currently publicly available through the Northwest RCE web resources and supports analysis for any of the published Francisella tularensis genomes.

Using PSAT

Use the web interface to select one of the Francisella tularensis genomes as the reference genome and the desired set of comparison genomes. You may enter a gene name, locus tag, description, or a range of genome coordinates to find genes to analyze. You can also select BLAST score threshold values to limit the list of homologs returned from the query.

If multiple genes are found that match your criteria, a list of these matches will be displayed along with details about each gene. You may browse and select genes from this list to retrieve results. The results page will include a table of homologs (as determine by BLASTp), grouped by bacterial genus. The list will be ordered based on the genes found in the same order between the reference genome and the comparison genomes. This ordering can serve as a rough prediction of synteny strength between the local region containing the gene of interest and the local region containing the homolog. Scores used for this ranking are also displayed in the table to give you a rough idea of how far the synteny may extend.

Below the table of results is a graphic visualizing the genomic regions surrounding the gene of interest and its homologs listed in the table. The homolog is aligned beneath the gene of interest and homologs in the surrounding region are colored to indicate which gene in the reference genome it has a BLAST hit with. You may also mouseover any gene to view gene details and additional BLAST hit details, if any, to use for further evaluation.

For more details, see the PSAT User's Manual.