Description

Teaching materials for the 2021 Microbiomes course at IST
April 2021
Author: Sandra Godinho Silva
sandragodinhosilva@tecnico.ulisboa.pt

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Outline:

Day 1: Bioinformatic tools for Genome Annotation

• Part 1: Bioinformatics: what are the tools available?

• Part 2: Bioinformatic tools for Genome Annotation

• Hands-on 1: Annotation with the COG database

• 1.1: Rast-WebMGA workflow

• 1.2 Join COG annotation with a R script
• 1.2.1: R Setup
• 1.2.2: Get started with R and RStudio

Download R script to join COG annotation: link

Day 2: Metagenome mining of secondary metabolite biosynthetic gene clusters (SM-BGCs)

• Study case: the marine bacterial Aquimarina genus

• Hands-on 3: Metagenome mining of SM-BGCs using antiSMASH and BiG-SCAPE

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Sources

The construction of these learning materials was inspired in the following sources:

• An Introductory Undergraduate course in Bioinformatics by Prof. Rob Harbert
• R Carpentries