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SOP032: Finding Genes that May Be Characteristics of a Phenotype

This procedure explains how to use the NMPDR SigGenes? page (Signature Genes Tool) to compare and contrast whole genomes with the goal of defining a phenotype.

• For example, what genes are characteristic of the El Tor-like biotype responsible for the seventh cholera pandemic?

The Signature Genes Tool requires you to specify a reference genome, an inclusion set, and an exclusion set. The tool looks for genes from the reference genome that are common in the inclusion set and uncommon in the exclusion set. Genes found by the tool are likely to be characteristic of the genomes in the inclusion set.

As the reference genome, select an organism that exemplifies the phenotype.

• For example, choose Vibrio cholerae strain N16961, which has the O1 serotype and El Tor biotype.

In the inclusion set, select any number of genomes (zero or more) that share the phenotype to compare with the reference genome.

• For example, include Vibrio cholerae strain MO10, which has the O139 serotype and closely resembles the El Tor biotype.

In the exclusion set, select any number of related genomes that do NOT share the phenotype. These will be contrasted with the reference genome.

• For example, choose Vibrio cholerae strain O395, which has the O1 serotype and classical biotype.

Leave the remainder of the settings at their default values, and click the Go button. A simplified version of the Signature Genes Tool input form is given below. You may use it to run the example, or to run an example of your own. The results will open in a new window or tab.

The tool searches the database to find every protein in the reference genome that has BidirectionalBestHits? (BBHs) with most of the genomes in the inclusion set. Then it compares those to the genomes in the exclusion set and removes from the results all proteins in the reference genome that have BBHs with most of the genomes in the exclusion set. For every protein in the reference genome, the tool computes a score from 0 to 1. A score of 1.000 means that the gene has a bidirectional best hit in every genome from the inclusion set and no bidirectional best hit against any genome in the exclusion set. When the sets are large, proteins with less than perfect scores will be returned in the results.

• For example, 76 proteins in Vibrio cholerae strain N16961 have bidirectional best hits with strain MO10, but not with strain 0395. These are a starting point for finding genes that may be responsible for pandemic virulence.

To run the search using similarities instead of bidirectional best hits, check the Use Similarities box. To see which genes matched each gene in the reference genome, check the Show Matching Genes box.