What?

Course objectives

By the end of the course participants should be able to:
• Explain the use of Bioinformatics
• Name the key Bioinformatics techniques and tools
• Locate important biological databases and retrieve data
• Use selected tools effectively to run specific Bioinformatics analyses
• Understand the strengths and limitations of the various techniques

Course modules

Introduction, Databases and Resources

  • Overview of bioinformatics and application areas – ‘What is bioinformatics and why is it important?’
  • Biological databases and resources (NCBI, EBI)
  • Advanced literature searching – PubMed
  • DNA analysis – e.g. sequence features, start site, restriction sites etc

Genomics

  • Genome sequences – sequencing technology and brief NGS overview
  • Genome browsers and annotation
  • Comparative Genomics
  • Human variation

Linux

  • Introduction to Linux, UNIX and the command line
  • Manipulating files – useful commands and tips
  • Permissions, groups, and process control

Sequence Alignment theory and application

  • Introduction to searching and sequence alignment
  • Pairwise sequence alignment
  • BLAST algorithm

Multiple Sequence Alignment

  • Applications of multiple sequence alignment
  • Choosing the right sequences with the right software

Protein Structural Bioinformatics

  • Introduction to protein structure and protein bioinformatics
  • Comparative modelling

Phylogenetics and Molecular Evolution

  • Historical perspective, mechanisms of molecular evolution, and speciation.
  • Traits, phylogenies, evolutionary models and divergence times.
  • Tree building with distance matrix methods. Parsimony approaches.
  • Tree building with maximum likelihood approaches. Bayesian viewpoint. Branch support measures.