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Bacterial Genomes: Accessing and Analysing Microbial Genome Data

Learn more about how genomic data and computational tools can help us understand and track disease-causing bacteria.

Bacterial Genomes: Accessing and Analysing Microbial Genome Data
  • Duration3 weeks
  • Weekly study5 hours
  • LearnFree
  • Digital upgradeFree
  • AccreditationAvailableMore info

Use computational tools to investigate microbial genomes

Applying increasingly powerful computation to genomics contributes to important medical breakthroughs.

On this course, you will discover the basic principles of microbial bioinformatics analysis, and comparative genomics. Using Artemis, a free genome browser, you will find out how to investigate whole bacterial genomes, and through the analysis of bacterial genes and proteins, you will explore the genomic features of pathogens.

By the end of this course, you will be able to use genomic data to increase your knowledge of microbial genomes.

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Skip to 0 minutes and 9 secondsResearch into bacterial genomes have been revolutionised by computer programmes. These programmes are in constant development, keeping up with the growing demands of researchers and technology. My name is Dr. Anna Protasio. I'm Dr. Christine Boinett. And I am Professor Pablo Tsukayama. Here at the Wellcome Sanger Institute, alongside collaborators from around the world, bioinformatitians and researchers work together to deliver the best tools for genome analysis. In this course, you'll learn one of these tools called Artemis, an open-source genome browser that's specially designed for bacterial genomes and their annotations. Together, we'll explore the different functions in Artemis and unlock the features so that we can better understand the biology of the organism. You will learn through a combination of articles, screencasts, and interviews.

Skip to 0 minutes and 54 secondsYou will join in productive discussions, sharing your findings and ideas with other learners. And together, we'll be working on a real research problem. Join us in this new adventure, when we find out what lies behind bacterial genomes.

Syllabus

  • Week 1

    From 11 May 2020

    Welcome, Reference genomes and introduction to Artemis

    • Welcome to the Course

      Welcome to the Course

    • Reference genomes: Genome assemblies, construction, representation, and reliability

      Multi-FASTA files, Reference and draft bacterial genomes

    • The bacterial genome browser Artemis

      Introduction to Artemis, an open source genome browser

  • Week 2

    From 18 May 2020

    Genome annotation, GC (guanine-cytosine) content, and data access

    • Genome Annotation

      Genome annotation and file formats

    • Genomic regions have different content of Gs and Cs

      GC (guanine-cytosine) content as used to identify regions of the bacterial genome with particular characteristics, Pathogenicity islands

    • Data access

      Accessing whole bacterial genomes freely available on the internet, Analysing viral SARS-CoV-2 genome using Artemis

  • Week 3

    From 25 May 2020

    Consolidation and Peer Review Project

    • Artemis further practice

      Practice more with Artemis and learn a few more functionalities

    • A real case study where Artemis saves the day!

      Case study of the use of Artemis: explore the annotation of a bacterial genome and compare annotations in two genomes

    • Assignment completion, sharing learning, and peer review

      Peer review: complete your project's report and share it with other learners

    • Project resolution, Week 3 and the Course Summary

      Discussion of some answers to the Project, Review of Week 3 and the Course's Learning.

    • Assessment, discussion, reflection and acknowledgments

      End of the course: complete the multiple choice assessment, join in the concluding discussion and reflection, Plan next steps

    • Acknowledgements

      Acknowledgements to the course team

Who is this accredited by?

Royal College of Pathologists
Royal College of Pathologists:

RCPath has approved this course for 15 CPD credits. This applies to medical staff and clinical scientists in career grade posts who are enrolled with one of the Royal Colleges for CPD purposes.

When would you like to start?

Most FutureLearn courses run multiple times. Every run of a course has a set start date but you can join it and work through it after it starts. Find out more

  • Available now

What will you achieve?

By the end of the course, you‘ll be able to...

  • Collect, access, and download whole bacterial genomes from public repositories
  • Investigate and navigate bacterial genomes and their annotation using Artemis
  • Identify genomic regions with low/high GC (guanine-cytosine) content, often associated with virulence
  • Perform simple comparative analyses between bacterial genomes

Who is the course for?

This course would benefit those interested in learning how to use tools to investigate bacterial genomes, and acquire bioinformatics skills to evaluate the role of microbial genes in disease. Using analytical tools to access and probe genomes, learners will find out how to perform comparative analyses of genes and their protein products.

The course will be of interest to undergraduates, post-graduates, researchers, bioinformaticians, microbiologists, and healthcare professionals. The opportunity to use online computational tools to probe bacterial genomes will also be of interest to teachers and their 16-18-year-old science and computing students.

Bacterial Genomes: From DNA to Protein Function using Bioinformatics is a recommended pre-requisite. Scientific terminology is explained.

What software or tools do you need?

This course will give you an opportunity to learn about and use Artemis, a free genome browser and annotation tool. To run this software effectively, you will require a computer (Windows, Mac or Linux) with 2GB RAM. The current version of Artemis requires version 1.11 of Java to run successfully. Java can be downloaded from this link.

What do people say about this course?

A highlight of the course is the project - it applies the newly acquired skill set.

Mqondisi Tshabalala
PhD student, Institute for Cellular and Molecular Medicine, University of 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 bacterial genetics and my interest is in understanding the development of resistance in bacterial pathogens using next generation sequencing techniques.

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.

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.

Learner reviews

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