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SOP033: Finding Genes that are Important in Specific Types of Pathogens

This procedure explains how to use the NMPDR SigGenes page (SignatureGenesTool) to compare and contrast whole genomes with the goal of defining what certain types of pathogens have in common. Such genes may be critical to the survival or virulence of the pathogens, making them useful drug targets? .

  • For example, what genes are common to GramNegative? respiratory pathogens?

The Signature Genes Tool requires you to specify a reference genome, an inclusion set, and an exclusion set. In this case, we will not be using an exclusion set. The tool looks for genes from the reference genome that are common in the inclusion set.

As the reference genome, select a commonly used strain of a relevant species.

In the inclusion set, select any number of genomes that share a phenotype with the reference genome.

  • For example, include all available strains of Chlamydophila pneumoniae, Haemophilus influenzae, Mycoplasma pneumoniae, Legionella pneumophila, and Pseudomonas aeruginosa to determine the core set of genes shared by these strains.

Leave the remainder of the settings at their default values and click the Go button. You may use the form below. The results will open in a new window or tab.

Reference Genome
Show genomes containing  
Inclusion Set