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

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

6,503 enrolled on this course

Bacterial Genomes: Comparative Genomics using Artemis Comparison Tool (ACT)
  • Duration3 weeks
  • Weekly study5 hours
  • LearnFree
  • Digital upgradeFree
  • AccreditationAvailableMore info

Gain experience in using the Artemis Comparison Tool for comparative genomics

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.

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Skip to 0 minutes and 9 seconds Welcome to this course in bacterial comparative genomics. My name is Dr. Ulrike Boehme. And I’m Dr. Christine Boinett. Comparative genomics is used to compare genomic features between different or similar organisms. In this course, we’ll be using a freely available software, known as the Artemis Comparison Tool, to compare bacterial genomes. There will be plenty of articles, screencasts and interviews to guide you through the process. You’ll also have the opportunity to join in constructive discussions with other learners and share your findings. These discussions will be especially useful in week three, where you’ll need to tackle a real research problem. Join us in this new adventure, where we delve further into bacterial genomes.

Syllabus

  • Week 1

    Introduction to Comparative Genomics and Artemis Comparison Tool (ACT)

    • Course Introduction

      Welcome to the course and meet you educators, Share what brings you here, Get started with resources you will need, Glossary

    • Comparative Genomics

      What is comparative genomics

    • Introduction to ACT

      What is ACT, ACT installation, Open your first comparison file, important things to remember

  • Week 2

    Working with ACT

    • Analysing already available data

      Opening DNA, annotation and comparison files into ACT, Conservation of gene order, Breaking the synteny, Bacteriophages cause insertions in the S.typhi genome, S.typhi bacteriophage insertions, How do inversions look like

    • Making your own comparison files

      What are comparison files? Making comparison files using doubleACT, Making comparison files using BLAST, Understanding the comparison file output

    • ACT in real life research scenarios

      Real research cases: application of Artemis Comparison Tool software

    • Hands on exercise

      Comparison between plasmids which have conserved backbones and variable cargo contents, or an equivalent comparison between some closed bacterial genomes

  • Week 3

    Peer-reviewed project

    • Introduction

      Introduction to peer-reviewed project

    • Whole genome comparison of M. tuberculosis and M. leprae

      Whole genome comparison of M. tuberculosis and M. leprae using ACT

    • Peer review project: Shigella pKSR100 vs E.coli 0157 plasmid

      Peer review project -Shigella pKSR100 vs E.coli 0157 plasmid peer-reviewed project

    • Assessment, discussion, reflection and acknowledgments

      End of the course Assessment, discussion and reflection

    • Acknowledgements

      Acknowledgements

Who is this accredited by?

Royal College of Pathologists
Royal College of Pathologists:

This course has been accredited by the Royal College of Pathologists for 15 CPD credits. Credits can be claimed at a rate of 1 credit per hour of engagement with this course.

When would you like to start?

Start straight away and learn at your own pace. If the course hasn’t started yet you’ll see the future date listed below.

  • Available now

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 the Artemis Comparison Tool (ACT)
  • Interpret results from already generated comparison files
  • Produce new comparisons and analyse results
  • Develop hypothesis based on results observation

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 recommended 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 the course.

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.

What do people say about this course?

This is an excellent course - pretty easy to follow and apply the tools.

Dr Michael Andrew Quail | Senior Staff Scientist - R&D Sequencing | Wellcome Sanger Institute | Cambridge UK

In Week 3, the Peer Review ...applies concepts learnt on ACT comparative genomics in real life clinical cases - this is a highlight of the course.

Mqondisi Tshabalala | PhD student | University of Pretoria | Pretoria, South Africa

Who will you learn with?

I am a researcher in parasitology and computational biology at the University of Cambridge. I am passionate about bioinformatics and how we can use these tools to answer questions in biology.

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

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.

I am the IT Manager for the Wellcome Genome Campus Advanced Courses and Scientific Conferences team. My interests lie in bioinformatics and its application to microbial genomics.

I am a graduate student at the Wellcome Sanger Institute, where I research the virulence and the molecular genetics of bacterial pathogens.

I am a Group Leader at the Wellcome Sanger Institute. I provide scientific oversight for this course. I am interested in bacterial evolution and the spread of infectious disease.

Who developed the course?

Wellcome Genome Campus Advanced Courses and Scientific Conferences

Wellcome Genome Campus Advanced Courses and Scientific Conferences provides open postgraduate courses and conferences focused on biomedicine.

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Wellcome Sanger Institute

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What's included?

Wellcome Genome Campus Advanced Courses and Scientific Conferences 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