epsSMASH Documentation#

Welcome to the documentation of epsSMASH, the extracellular polymeric substance Secondary Metabolite Analysis SHell.

epsSMASH is built on the antiSMASH framework, a widely used tool for detecting Biosynthetic Gene Clusters (BGCs) in microbial genomes. BGCs often contain all the genes required for the biosynthesis of one or more natural products, something antiSMASH has leveraged to predict the genomic potential for various secondary metabolites such as those produced by nonribosomal peptide synthetases and polyketide synthases.

epsSMASH allows for the detection of BGCs responsible for the production of Extracellular Polymeric Substances (EPS) in microbial genomes. EPS are complex polymers, mainly composed of polysaccharides, proteins, and nucleic acids, which form a an extracellular matrix around and between cells. This matrix is critical for biofilm formation, providing resilience against environmental stresses and immune defenses.

Since biofilms are the default mode of living for most microbial communities, research into the polymers which make up the extracellular matrix is highly relevant for the field of microbial ecology as a whole.

In this initial version of epsSMASH (Version 1.0) we have focused only on the detection of exoPolySaccharide (exoPS) BGCs. In future versions we hope to add detection modules for extracellular proteins and nucleic acids as well.

How to Use epsSMASH - Public Web Version#

The easiest way to get started with epsSMASH is to use the public webversion.

See the USING EPSSMASH.ORG section of this documentation for more information on how to submit epsSMASH jobs and interpret the HTML output.

The Glossary provides a list of the rules used by epsSMASH as well as supporting information on the rules. The exoPS categories page provides a detailed description of the exoPS categories used by epsSMASH.

Frequently asked questions can be found in the FAQ section. Please consult the FAQ before raising an Issue on the epsSMASH GitHub page.

How to Use epsSMASH - Local Installation#

If you need to analyse many genomes or run custom analyses, please download and install a local copy of epsSMASH. Running large-scale analyses locally instead of on the webservice reduces the load and helps us to keep epsSMASH available for everybody.

For instructions on how to install epsSMASH locally, and for tips on how to run it, please see the Install Guide.