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SOP032: Finding Genes that May Be Characteristics of a Phenotype

This procedure explains how to use the NMPDR SigGenes page (SignatureGenesTool) 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.

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

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

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.

Reference Genome
Show genomes containing  
Inclusion Set