PSAT User's Manual

4. Analyzing Genomic Neighborhoods and Potential Gene Clusters

Below the table of homologs in the Results page is the graphic visualizing genomic neighborhoods. The genomic regions can be expanded or collapsed by clicking the expand or buttons at the left of the graphic. Each displayed region corresponds to a homolog listed in the table. The regions are drawn in the same order in the which homologs are listed. Here we describe the different components of the graphic and how it can be used to analyze gene context.

Take a look at the various features of the graphic. (The table of results can become quite wide. If part of the graphic is cut off or you can't see the scrollbar at the right of the graphic, try widening your browser window. If the window is still too small you may need to increase your screen resolution)

Understanding the Genomic Neighborhoods graphic

You will now walk through some of these features to see how they can be used for your analysis

1. Note that a region of the reference genome F. novicida is drawn at the top of the graphic, with the selected query gene pilQ drawn at the center of this region. All genes in the reference genome are arbitrarily assigned a color. Genes found on the forward strand are drawn above the horizontal axis, and those found on the reverse strand are drawn below. The coordinates of each gene can be estimated using the scaler drawn at the very top of the image. The gene name or locus tag is displayed above each gene. All syntenic regions drawn below are aligned to this reference genome region


2. Scroll through the graphic displaying the genomic neighborhoods for homologs using the inset scroll bar. The scrolling feature allows you to easily align each potential syntenic region with the reference genome. Compare the regions shown in the graphic and the results in the table of homologs. The results should appear in the same order which can be most easily verified by comparing the bacterial species indicated in the first column of the table and on the right side of the graphic.
   
   The coordinates of the genome region displayed for each comparison genome are drawn in gray at both ends. An arrow at the left end indicates the direction in which the genome is drawn, an arrow pointing right indicating the same direction as the reference genome, and an arrow pointing left indicating the opposite direction (drawn reversed and inverted). For example, the pilQ gene is found on the reverse strand in F. novicida and its ortholog on the forward strand in F. holarctica. The arrow therefore points left to indicate that the region has been drawn reversed and inverted such that gene order in the region corresponds. Note that the coordinates of the displayed region also indicate this reversal (the coordinate on the left is greater than the one on the right).
   
   The color of the genes in each region indicate which gene in the reference genome it is homologous with. If a gene is gray, it indicates that it is not a homolog with any of the genes displayed in the reference genome (this does not mean it does not have a homolog in another region of the reference genome, but not in the immediate neighborhood). Because any gene that is a homolog to a gene displayed in the reference genome graphic is highlighted, PSAT can help researchers identify potential gene clusters in which the order of genes are slightly scrambled.


3. Mouseover one of the genes. A popup should appear. At the top of the popup are some details about the gene you are mousing over, including gene name, locus tag and description. If this gene is a homolog to a gene in the reference genome, details are also displayed about the query gen and BLAST hit score values for the gene pair. If multiple hits are found in the displayed genomic region, information about each hit is displayed (however, the gene color is determined by the top hit). The mouseovers can help with the analysis of each potential syntenic region by allowing you to inspect the ordering of homologs, assess the strength of each alignment, and compare product descriptions, if any.

Graphic Display Options

There are a couple of display options for the graphic that are found in the upper right hand side.

1. The Zoom tool allows you to modify the size of the region drawn (in nucleotide bases). 25K bases is the default region size. Select 10K to view a smaller region size.


2. Now select 50K to view a larger region size. Since there are a large number of genes in this region, they may appear crowded in the graphic. You can increase the size of the image width to be able to view the genes more clearly. Select ++ under the Image Width option to increase the width. Now decrease the width slightly by selecting -.

Printing and Saving Results

There are a few options for printing or saving the results in the graphic. These options are available in the bar above the graphic.

1. Download file: Download the graphic as a .pdf file
2. Printer friendly: Open a printer friendly version of the graphic in a new web browser window. This version does not include links, mouseovers, and does not have the scrollable bar for scrolling through the genomes to compare next to the reference genome.
3. Tab delimited: A tab delimited text format of the homologs in the region. This lists the genomes displayed in the graphic with the locus tag of the homologs in the genomic neighborhood. Homologs that do not meet the specified BLAST threshold score values are shown in parentheses.