PSAT User's Manual

3. Inspecting Gene Homologs and Homolog Clustering Scores

The Results page displays both a table of homologs found for the specified gene and a graphic displaying the genomic neighborhood surrounding the gene and its homologs. We will first inspect the table of results. (The table of results can become quite wide. If part of the table gets cut off, try widening your browser window. If the window is still too small you may need to increase your screen resolution)

Inspect the various components of this table.

We will now go through some of the interesting aspects of the results table

1. The number of BLAST hits that met our specified BLAST score threshold values in our specified comparison genomes is displayed in the table header (see current settings in italics below this number). Since we used the default setting to display all hits, the number may include multiple hits from the same genome. You can select the view top hits only link to only show the top hits in each genome, eliminating any lower scoring hits. For our current query, the number of total and top hits is the same, indicating there are likely no duplicated regions that meet the specified threshold values.


2. The details for the selected gene pilQ is shown in the top row of the table, colored beige. The listed details, such as position, strand, length, name, locus tag and description, have been taken directly from the .ptt file published on NCBI. The gene position index value was determined based on the published position of all genes in the genome


3. The homologs that meet the specified criteria are listed in the rows below the selected gene. Details about each homolog from NCBI published data (.ptt files) are listed directly below that of the query gene to faciliate comparison. The BLAST score values for the hit are shown in the columns colored gray.
   
   Note that for many of these homologs, the annotated gene name is also pilQ or the product description is very similar to that of the gene in F. novicida.
   
   You may collapse and expand the list of homologs by clicking the to collapse and the to expand.


4. The homologs are ordered by the homolog clustering scores that are pre-calculated by the tool. Higher scores predict stronger synteny, so homologs with the largest scores are shown first. The score is defined as the number of consecutive, uninterrupted gene homologs neighboring a particular homolog pair.
   
   See Implementation Details for more detailed information on how the homolog clustering scores were calculated. The scores are displayed at the end of each row.


5. Note that the list of homologs have also been grouped by bacterial genus to help organize the results in a manner that is easier to browse. As you might expect, the homologs found in the Francisella genomes scored the highest and are therefore displayed at the top.


6. Reorder the results based on another value such as a BLAST hit score, or by Genome. Select the column headings that are links to see how the results are reordered. Selecting e-value will sort by lowest score first, and selecting any of the other BLAST score fields will sort by highest score first.
7. You can also select which homologs to display genomic neighborhoods for in the graphic by checking and unchecking the checkboxes at the left of each row. For now, leave all homologs checked.


8. The graphic should currently display the genome region surrounding the query pilQ gene in F. novicida. To view the genomic neighborhoods surrounding the homologs in the comparison genomes, click the expand button to the left of the graphic or click on the Update Graphic button at the bottom of the table of homologs. Next you will explore this expanded graphic to analyze potential syntenic regions.