PSAT User's Manual
2. Browsing List of Genes
We will now inspect the list of genes that the tool has found to match our search settings. Note that this page is only displayed if the tool has found multiple gene matches. If only one gene was found, you would be immediately directed to the Genomic Neighborhoods page for that gene. This list of gene results allows you to determine and select which gene you would like to compare the genomic neighborhood with other genomes.
We will use this page to select the pilQ gene to explore the genomic neighborhood for. However, it is also interesting to inspect other areas of this page.
- Review the table at the top of the page. Verify that the settings we set in the input page match what is displayed here. Note that you can select the Edit Settings link to make any modifications you see necessary.
- Note that 13 genes were found that matched our criteria for the gene name to contain the string 'pil'
- The Gene # column indicates the position order index of a gene within the genome. Quickly scanning this column, you may note that several of the genes are found directly adjacent to each other (genes #s 1112-1116).
- Note details such as protein lengths and product descriptions which can also be interesting.
- Note the number of BLAST hits for each gene. The number displayed is only the number of hits found that meet all of our specified score thresholds in our selected comparison genomes (see grey section in the table at the top of the page to review our settings). Changing these setting values can change the number of hits indicated here.
The number of homolog hits found is specified and the number genomes in which hits were found. If the number of hits is more than the number of genomes, then some genomes may have duplicated regions. Also note that these numbers only reflect the number of hits with a homology clustering score of at least 2.
- Find the pilQ gene. Mouseover this row to highlight it yellow, and click to bring up the Genomic Neighborhoods page.
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