Bacterial Genomes: Comparative Genomics using Artemis Comparison Tool (ACT)

03 August 2021–01 July 2022

FutureLearn platform, online

Learn to use comparative genomics to improve your knowledge of microbial genomes.

Overview

  • Duration: There is no longer a live period for this course, and there will be no live monitoring of the forums, but you can still join and complete the course throughout 2021/22
  • Free
  • Certificate of achievement available on satisfactory completion

Why join the course?

Disease outbreaks are still a big problem in our modern world. Comparison between two or more bacterial genomes can help improve understanding of the causes of pathogenicity and outbreaks of disease caused by bacteria.
On this course you will learn how to use the free Artemis Comparison Tool (ACT). Developed at the Wellcome Sanger Institute, ACT will help you to visualise the comparison of genomes and analyse the results.

Who is the course for?

This course would benefit those interested in learning how to use tools to investigate and research bacterial genomes, and acquire bioinformatics skills to evaluate the role of microbial genes in disease. Learners will gain experience in comparative genomics, using the Artemis Comparison Tool to probe, visualise and compare genomes, and analyse the results.

This course will be of interest to anyone interested in microbiology, including undergraduates, post-graduates, biomedical researchers, microbiologists, bioinformaticians, teachers, and healthcare professionals.

The opportunity to gain experience in using the Artemis Comparison Tool, a computational tool designed for comparative genomics, will also be of interest to all those who have studied our pre-requisite courses: those with an interest in genomics and disease outbreaks, teachers and their 16-18-year-old science and computing students.

Ideally, you will have completed Bacterial Genomes: From DNA to Protein Function Using Bioinformatics and Bacterial Genomes: Accessing and Analysing Microbial Genome Data before joining this course.

Programme

What topics will you cover?

Week 1

  • Introduction to comparative genomics
  • Introduction to ACT

Week 2

  • Analyse available data
  • Generate your own comparison files
  • Make your own comparisons in ACT

Week 3

  • Identify pseudogenes in Mycobacterium leprae using ACT
  • Peer review project: Comparative genomics on two clinically relevant plasmids from Shigella

 

What will you achieve?

By the end of the course, you’ll be able to…

  • Explain the advantages of comparative genomics
  • Explore basic tools of ACT
  • Interpret results from already generated comparison files
  • Produce new comparisons and analyse results
  • Develop hypothesis based on results observation

 

What software or tools do you need?

This course will give you an opportunity to learn about and use Artemis Comparison Tool (ACT), a free tool used to display pairwise comparisons between two DNA sequences. To run this software effectively, you will require a computer (Windows, Mac or Linux) with 2GB RAM. The current version of ACT requires version 11 of Java to run successfully. Java 11 can be downloaded from this link. Older versions of ACT require Java 8 to run successfully. Java 8 can be downloaded from this link.

Educators

Lead Educators

Dr Anna Protasio
I am a researcher in parasitology and life sciences. I am passionate about bioinformatics and how we can use these tools to answer questions in biology.

Dr Christine Boinett
I am a researcher in bacterial genetics and my interest is in understanding the development of resistance in bacterial pathogens using next generation sequencing techniques.

Dr. Ulrike Böhme
I am a researcher in parasitology at the Wellcome Sanger Institute where I work as biocurator for Plasmodium genomes.

Dr. Pablo Tsukayama
I am a professor of microbiology at Universidad Peruana Cayetano Heredia and a visiting research scholar at the Wellcome Sanger Institute. I study how pathogen populations evolve and spread in Peru.

Martin Aslett
I am the IT Manager for the Wellcome Connecting Science Courses and Conferences team. My interests lie in bioinformatics and its application to microbial genomics.

Matthew Dorman
I am a graduate student at the Wellcome Sanger Institute, where I research the virulence and the molecular genetics of bacterial pathogens as part of the Infection Genomics programme.

What's included

Wellcome Connecting Science are offering everyone who joins this course a free digital upgrade, so that you can experience the full benefits of studying online for free. This means that you get:

  • Unlimited access to this course
  • Includes any articles, videos, peer reviews and quizzes
  • Tests to validate your learning
  • A PDF Certificate of Achievement to prove your success when you’re eligible

Course trailer

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