Automated Sequence Analysis

Code: GEM6040, Offered By: Research Study Skills

Open To - University-wide

Semester Taught - Spring Semester

DNA and protein sequence analysis provides enormous insight into biological processes and can even be used to design new drugs. Using in silico bioinformatics tools it is possible to predict functions, model interaction and even to design potential new drugs. This module will equip students with the analytical and practical skills to manipulate DNA and protein sequences in useful ways. Through visualization of 3D molecular structures, they will understand how proteins function through their interactions with other molecules. Topics will include: storing and retrieving biological sequence data, DAN manipulation in silico, principles of molecular structure; visualizing biological molecules in 3D using Pymol; an introduction to computer assisted drug design. The module will be delivered largely through computer laboratory-based sessions, private study and an introductory seminar. Assessment will be via a written assignment.

Researcher Development Framework Categories:

A1) Knowledge base
A2) Cognitive abilities
A3) Creativity

B2) Self-management

Teaching Methods

The sessions will consist of interactive, practical sequence analysis classes with an instructor. The instructor will introduce each topic briefly and demonstrate each type of analysis. Students will carry out similar practical analysis with the instructor at hand to oversee and guide the class. Self study will further re-inforce and extend the students' knowledge and experience of analysing biological molecules in silico.


Students will be assessed through an assignment which will test their ability to analyze a given biological sequence, predict the likely function an 3D visualization. The assessment will test their ability to apply the knowledge and critical analytical skills taught during the course. They will be given raw data and will be required to produce an independent analysis of the biological system presented to them. The work to be handed in by the students will consist of electronic files illustrating the results of their analyses including molecular graphics files and text describing how they arrived at their results.

Aims Objectives

This unit will provide students with the tools to analyse biological sequences, predict functions and the impact of mutations. Students will also study basic molecular interactions and be introduced to computer-assisted drug design technologies. The unit will present both experimental and theoretical approaches to these topics.

Learning Outcomes

By the end of the unit, students will be able to demonstrate the ability to:
- Compare and analyse biological sequences in sillico.
- Infer biological function from sequence data
- Identify important motifs in new sequence sets
- Predict the impact of sequence change on biological function
- Critically review predicted biological structures & complexes
- Visualize and manipulate 3D structures using molecular graphics software.

Other Information

Module Dates 2019-2020

Thursday 23rd April 2020, 10.00-12.00, Seminar Room 9, C Floor, Medical School
Friday 24th April 2020, 09.00-12.00, Computer Room B56, Firth Court
Friday 1st May 2020, 09.00-12.00, Computer Room B56, Firth Court
Friday 8th May 2020, 09.00-12.00, Computer Room B56, Firth Court
Friday 15th May 2020, 09.00-12.00, Computer Room B56, Firth Court
Friday 22nd May 2020, 09.00-12.00, Computer Room B56, Firth Court

You must be able to attend all the above sessions - this module is not available on a drop in, drop out basis.

Staff Contact

Prof Jon Sayers  


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