Tutorials for Using RadicalSAM.org

This page provides information on how to use the resources on this site (which were developed using the EFI web tools).

RadicalSAM.org Overview

RadicalSAM.org empowers researchers in the field of radical SAM enzymology to discover novel functions of uncharacterized members of the RSS by democratizing the genomic enzymology tools. This video provides a tour of the site and encourages the user to explore the tools using their own radical SAM enzymes.

Maneuvering the Dataset Using the Explore Tab

The Explore tab gives the user the ability to maneuver through the enormous protein dataset in RadicalSAM.org. This video provides a tour of the Explore tab and details the various tools in the tab.

Overview of the Genome Neighborhood Diagram Viewer

GNDs are powerful tools in determining the potential function of a radical SAM enzyme. This video describes their use and how they have been incorporated into RadicalSAM.org.

Determining Points of Isofunctionality using "Dicing"

RadicalSAM.org uses SSNs generated at a series of increasing alignment scores, through a process known as dicing, to assist the user in determining points of isofunctionality in the radical SAM superfamily. This video provides a brief description of that process.

Searching for a Specific Radical SAM

The Search tab enables the user to search for a specific radical SAM in RadicalSAM.org. This video provides a tour of the Search tab and describes how a user can find useful information about their radical SAM enzyme.

A "Dicing" Case Study

This video provides a tutorial on determining an isofunctional alignment score for a radical SAM of interest using PqqE, the PqqA peptide cyclase in pyrroloquinoline quinone (PQQ) biosynthesis, as a case study.