For publication of results, please cite:
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

Analysis Options

1. Select Reference and Comparison Genome(s):

Genomes last loaded from NCBI on 2010-01-25
Reference Genome Comparison Genome(s)
Select a genus:


Select a species:


Selected reference genome:
 Select a genus or all genomes:


Select species:


Selected comparison genomes:

2. Specify an analysis method and any necessary options:

Find homologs for specific gene(s) Get homolog list for a complete genome Compare multiple genomes Determine homology statistics
Browse homologs for specific gene(s) in the the reference genome that are found in the selected comparison genomes. Specify constraints to search for these genes to analyze below:
Gene name
Locus tag
Description
Start position range to
For all genes in the reference genome, get a list of homologs in the selected comparison genomes meeting specified alignment score thresholds

Selecting only a couple Comparison Genomes is recommended for this analysis.

Select an output format:
HTML table
Tab delimited text file
 Compare multiple genomes by determining genes with homologs in some genomes but not in others

Selecting only a couple Comparison Genomes is recommended for this analysis. Selecting 'All Genomes' is not allowed for this analysis.		 Compare genomes based on the proportion of genes in the reference genome with homologs in the comparison genomes

3. Modify BLAST alignment score thresholds for finding gene homologs:

e-value < 1e-1720.110
bit score > 60020020
% identity > 503010
(select one)

4. Select Display Options

Limit number of hits to display Limit results based on top hits Limit results based on homolog cluster scores List hit count in gene list
Display only first hits Show only top hits for each comparison genome
Show all hits for each comparison genome 		Only show hits with a homolog clustering score of at least
Display number of BLAST hits
Display number of genomes with hits


© University of Washington 2008