module specification

The module uses online databases and software to extract, analyse and interpret DNA and protein sequences and to model structures of proteins.

This module aims to:
• Provide familiarity with the primary databases and common software packages used to analyse DNA, RNA and protein sequence, expression and structure, within and across genomes;
• Develop informatics skills for extracting, analysing and presenting data to extract biological knowledge;
• Apply the principles of macromolecular, and in particular protein, structure to the building f molecular models using modelling and graphics software;
Examine applications of modelling with emphasis on understanding the interactions between proteins and other molecules of biological or synthetic origin.

LO 1 - 3

Primary and secondary databases in areas of biology, genetics, pharmaceutical science and biomedical science including gene and protein sequence databases, 3-D structure databases, genome databases and disease databases.
Application of online servers to sequence alignment and analysis of gene and protein databases, RNA structure prediction, molecular modelling and phylogenetic classification and pharmacogenomics analysis. Docking and drug design.

Students will be presented with material in interactive teacher-led activities in the form of lectures and computer-based tutorial sessions. Student learning time will be used for assignments, data analysis and the preparation of coursework assignments.

PDP: on completion of this module students will write an evaluation of how the module allowed them to develop skills in data-mining, knowledge extraction and presentation in bioinformatics

After completing the module students should have developed:
1. An advanced systematic knowledge of the theoretical aspects of bioinformatics and molecular modelling and an up-to-date knowledge of current developments and knowledge in this area;

2.  An ability to apply knowledge learnt to bioinformatics and molecular modelling problems involving the extraction, analysing and presentation of data as appropriate;

3. Intellectual skills, through reflection and through practice by engagement with the module learning materials.

Module is assessed by two coursework components which provide formative as well as summative assessment. Module must be passed overall with pass mark of 50%.

Component    Learning outcomes
Data Analysis 1                1,2,3
Data Analysis 2                1,2,3

Formative feedback given throughout computer-based tutorial sessions. Summative feedback on returned coursework.

Key Online Resources:
Primary DNA and Protein Sequence Databases
GenBank: www.ncbi.nlm.nih.gov/Genbank      EMBL:       www.ebi.ac.uk/embl
DDBJ:       www.ddbj.nig.ac.jp                          UniProt:   www.uniprot.org
Protein database at the NCBI: www.ncbi.nlm.nih.gov/protein

Secondary Protein Databases and Sequence Alignment Servers
PROSITE:   www.expasy.ch/prosite                    PRINTS:www.bioinf.manchester.ac.uk/dbbrowser/PRINTS
Pfam:        pfam.sanger.ac.uk                            
SMART:     smart.embl-heidelberg.de
NCBI BLAST and PSI-BLAST:   www.ncbi.nlm.nih.gov/blast                      
BLAST and FASTA@EBI:       www.ebi.ac.uk/Tools/sss/            
Clustal Omega:     www.ebi.ac.uk/Tools/msa/clustalo/

Protein Structure Prediction and Other Important Websites
SWISS-MODEL:  www.expasy.org/swissmod/SWISS-MODEL.html
3D-JIGSAW:        bmm.crick.ac.uk/~populus/
I-TASSER:            zhanglab.ccmb.med.umich.edu/I-TASSER/            
Protein Data Bank:   www.rcsb.org/pdb             PHYRE2:               www.sbg.bio.ic.ac.uk/phyre2
Swiss PDB viewer:     spdbv.vital-it.ch               SwissDock:            www.swissdock.ch

Bibliography:
Baxevanis A.D. and Ouellette B.F.F. (eds.) (2005) Bioinformatics.  A Practical Guide to the Analysis of Genes and Proteins, (3rd edition) John Wiley.
Bishop M.J. (ed.) (1999) Genetics Databases, Academic Press.
Bromham, L.  (2008)  Reading the Story in DNA a beginner’s guide to molecular evolution.  Oxford University Press.
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.
Gopal, S., Haake, A., Jones, R.P. and Tymann, P. (2009) Bioinformatics: A Computing Perspective, McGraw-Hill.
Gu, J. and Bourne P.E. (eds.) (2009) Structural Bioinformatics (2nd Edition) Wiley-Blackwell.
Hodgman, C., French, A. and Westhead D.R. (2009) Bioinformatics (Instant Notes) BIOS Scientific Publishers.
Krane D.E. and Raymer M.L. (2002) Fundamental Concepts of Bioinformatics, Benjamin Cummings.
Lesk A.M. (2014) Introduction to Bioinformatics (4rd Edition), Oxford University Press.
Mount, D.W. (2004) Bioinformatics; Sequence and Genome Analysis (2nd Edition) CSHL Press.
Pevsner, J. (2015) Bioinformatics and Functional Genomics, (3rd Edition) Wiley-Blackwell.
Selzer, P.M., Marhofer, R.J. and Koch, O. (2018) Applied Bioinformatics: An Introduction (2nd Edition) Springer.
Zvelebil, M. and Baum J.O. (2008) Understanding Bioinformatics, Garland Science.