Intended audience

The course is aimed at individuals from a Molecular Biology background who have a basic understanding of Biochemistry and/or Genetics and would like to become basic Bioinformatics users. A base line level of the understanding of the central dogma of molecular biology (i.e. DNA to RNA to Protein) is a requirement.

By the end of the course participants should be able to:

• Explain the use of Bioinformatics
• Name 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

Databases and Resources

• Biological databases and resources (NCBI, EBI)
• Advanced literature searching – PubMed
• DNA analysis – e.g. sequence features, start site, restriction sites etc
• Protein function classification

Linux

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

Sequence Alignment

• 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

Genomics

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

Molecular Evolution and Phylogenetics

• 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.

Additional elements of the course:

Staff Training

Introduction Week

Wrap up Session

Bonus Module – Gene Expression

Course logistics

Training Material Availability:

Training materials for this course are available here: https://zivahub.uct.ac.za/projects/Introduction_to_Bioinformatics_Training_Course_Materials/131552. Should you re-use any of these materials, please ensure that both the author/s of the material AND H3ABioNet are clearly credited.

Materials have been made available as a single archive per module containing lecture slides, transcribed videos, practical assignments and any other resources important to complete each module:

Module 1: Databases and Resources

• https://zivahub.uct.ac.za/articles/educational_resource/IBT_Module_1_Databases_and_Resources_Training_Material_Archive/19106741 

Module 2: Linux

• https://zivahub.uct.ac.za/articles/educational_resource/IBT_Module_2_Linux_Training_Material_Archive/19106744 

Module 3: Sequence Alignment

• https://zivahub.uct.ac.za/articles/educational_resource/IBT_Module_3_Sequence_alignment_Training_Material_Archive/19106750 

Module 4: Multiple Sequence Alignment

• https://zivahub.uct.ac.za/articles/educational_resource/IBT_Module_4_Multiple_Sequence_Alignment/19106759 

Module 5: Genomics

• https://zivahub.uct.ac.za/articles/educational_resource/IBT_Module_5_Genomics/19106762 

Module 6: Phylogenetics (2018 - 2021)

• https://zivahub.uct.ac.za/articles/educational_resource/IBT_Module_6_Phylogenetics/19106765 

Module 6: Structural Biology (2016 only)

• https://zivahub.uct.ac.za/articles/educational_resource/IBT_Module_6_2016_Structural_Biology/19129892 

Introduction Week

• https://zivahub.uct.ac.za/articles/educational_resource/IBT_-_Introduction_Week_Training_Material_Archive/19106738 

Wrap Up week

•  https://zivahub.uct.ac.za/articles/educational_resource/Wrap_up_Week/19106768 

• 2016
• 2017
• 2018
• 2019
• 2020
• 2021