This tutorial outlines the various online biological databases and their uses as well as an introduction to homology terminology and searching using BLAST.
Learning outcomes
- Discuss the basis of antimicrobial resistance mechanisms and ays to detect them from genomic data
- Identify the primary virulence factors and ways to detect them from genomic data
- Define plasmids and their primary contents and ways to detect them from genomic data
- Use AbritAMR or similar to detect AMR and virulence factors
- Use PlasmidFinder to detect plasmid sequences in genome assemblies
Prerequisites
- It is recommended that you have Notepad++ (Windows) or BBEdit (Mac) for viewing fasta files; most linux default editors can do this.
- It is recommended that you have followed the Concepts in Computer Programming, UNIX tutorial (basics) and Setting up and using conda tutorials if you are going to do the UNIX-based worksheets.
Approximate time to finish tutorial
- Lecture: 20 mins
- Tutorials: 30 mins
Presentation
During the presentation there are points to stop and do exercises, which are linked below. The answers to the questions in the exercises are linked within each one.
Worksheets
Predicting pathogenic features using AbritAMR and PlasmidFinder via UNIX
Predicting pathogenic features using ABRicate and PlasmidFinder via Galaxy and the Web
Other tools and videos
- PlasForest
- Random forest based classification of plasmids
- Antismash: webserver; github link (for use in UNIX)
- Tool for finding secondary metabolites in genome assemblies
- IslandViewer 4
- Tool for finding genomic (including pathogenicity) islands