module specification

The module uses online public databases and software to extract, analyse and interpret nucleic acid and protein sequences and to model the structures of RNA and protein sequences. Genomics, in particular, with an emphasis on pharmacogenomics and phylogeny are covered. 

AS5005

The module uses online public databases and software to extract, analyse and interpret nucleic acid and protein sequences and to model the structures of RNA and protein sequences. Genomics, in particular, with an emphasis on pharmacogenomics and phylogeny are covered. 

The primary and secondary databases in biology including protein and gene sequences, protein structures, genome databases, disease databases - content, structure of files, links and other information.
Software for sequence analysis, including screening gene and protein databases, comparison of sequences, identification of functional domains, classification, phylogenetic analysis, RNA structure prediction.
Principles of protein architecture – review the role of non-covalent forces in the formation of secondary, tertiary and quaternary structures; protein folds and domains; folding and stability; membrane proteins; protein movement; protein complexes.
Software for analysis of known protein and nucleic acid structure.
Modelling protein structure; structure prediction by homology modelling; other approaches to prediction; probing active sites; protein interaction with other biomolecules; both proteins and drugs in particular. Protein-protein interactions and systems biology.
 

Students will be presented with material in interactive teacher-lead activities in the form of lectures (22 hours), and IT tutorials (22 hours).  Student learning time will be used for class assignments,  data analysis and preparation for coursework assignments (116 hours).

On successful completion of this module students will be able to:
1. Critically analyse the type of information contained within different primary and secondary databases and be able to extract appropriate biological information.
2. Select appropriate software for informatic analysis and present the output in a useful form with biological context.
3. Evaluate the important factors which determine the structure of, and interactions between, different types of biological molecules.
4. Analyse standalone structures and complexes between different structures utilising graphics and modelling software.
5. Critically analyse results obtained from the running of bioinformatics programs

The module will be assessed by means of two coursework components, which will provide formative as well as summative assessment. To pass the module, students need to achieve a minimum aggregate mark of 40%.  If the module is passed on reassessment, then the maximum mark awarded will be 40%.

The first assignment (50% of the overall module mark) will involve the use of software to analyse gene and protein primary structure. The second assignment (50% of the overall mark) will involve the use of modelling and graphics software to predict and display protein structures and explore interactions of proteins with ligands, drugs or other biomolecules.

Campbell A.M. and Heyer L.J. (2006) Discovering Genomics, Proteomics and Bioinformatics (2nd Edition) Pearson Benjamin Cummings.
Dardel, F. and Kepes, F. (2006) Bioinformatics: Genomics and post-genomics, Wiley.
Hodgman, C., French, A. and Westhead D.R. (2009) Bioinformatics (Instant Notes) BIOS Scientific Publishers.
Lesk A.M. (2008) Introduction to Bioinformatics (3rd Edition), Oxford University Press.
Lesk A.M. (2010) Introduction to Protein Science: Architecture, Function and Genomics, (2nd Edition), Oxford University Press.
Mount, D.W. (2004) Bioinformatics; Sequence and Genome Analysis (2nd Edition) CSHL Press.
Pevsner, J. (2009) Bioinformatics and Functional Genomics, (2nd Edition), Wiley-Blackwell.
Zvelebil, M. and Baum J.O. (2008) Understanding Bioinformatics, Garland Science.

Plus numerous websites – as detailed in module booklet.