Mohammed Abdul Jawad

9 months ago · 3 min. reading time · visibility ~10 ·

chat Contact the author

thumb_up Relevant message Comment

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

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

FREE ONLINE COURSE (with a PDF Certificate of Achievement to prove your success when you’re eligible)

  • Duration: 3 weeks

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


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.


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?

f71eff45.jpg

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.


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.


Who will you learn with?

  • Dr. Anna Protasio: 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. 
  • Dr. Ulrike Böhme: I am a researcher in parasitology at the Wellcome Sanger Institute where I work as biocurator for Plasmodium genomes. 
  • 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.
  • Martin Aslett: 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.
  • Matthew Dorman: I am a graduate student at the Wellcome Sanger Institute, where I research the virulence and the molecular genetics of bacterial pathogens. 
  • Professor Nicholas Thomson: 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.


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

To register and join the course, visit: https://www.futurelearn.com/courses/bacterial-genomes-comparative-genomics-act


thumb_up Relevant message Comment
Comments

More articles from Mohammed Abdul Jawad

View blog
3 months ago · 1 min. reading time

Wellness Challenge Ideas

WellRight’s wellness activities and challenge idea ...

3 months ago · 1 min. reading time

Improving Data Quality and Efficiency and Changing Pharmaceutical Analysis

FREE WEBCAST · Available On Demand · WEBCAST TITLE ...

3 months ago · 1 min. reading time

How to Stop Good Pharmaceutical Formulations Going Bad

FREE ON-DEMAND WEBINAR · Submit details to watch n ...