| CODE | PHB3504 | ||||||||
| TITLE | Bioinformatics | ||||||||
| UM LEVEL | 03 - Years 2, 3, 4 in Modular Undergraduate Course | ||||||||
| MQF LEVEL | 6 | ||||||||
| ECTS CREDITS | 4 | ||||||||
| DEPARTMENT | Physiology and Biochemistry | ||||||||
| DESCRIPTION | This study-unit shall explore the many practical uses and applications of Bioinformatics. These include (but are not limited to) genome assembly, gene function, gene prediction and annotation, RNA and protein expression, sequence alignment, comparative genomics, biological networks (e.g. signalling, metabolic, protein-protein interaction networks, protein structure prediction, systems biology, phylogeny (and evolution), and drug discovery. The vast amount of data generated by biological experiments critically require the use of computational tools for analysis and, hence, the discovery of novel insights. Bioinformatics is a data-intensive interdisciplinary field, involving molecular biology, genetics, computer science, mathematics, and statistics, which aims to provide these tools. This study-unit will offer perspectives from two parallel streams: molecular biology and computer science. Popular bioinformatics tools will be described, including their underlying algorithms. Moreover, biological implications of results will be explained. Throughout this unit student will be guided using practical, real-world examples. Study-unit Aims: This study-unit aims to take students through a number of practical scenarios which may be encountered in a molecular biology project. Bioinformatics tools will be used to analyse sequence and structural data for genes and proteins. The theoretical underpinnings of these tools will be explained (e.g. what the result scores mean, how they are calculated etc.). This study-unit is pivotal for the successful completion of any modern-day molecular biology project. Its focus is on using bioinformatics tools rather than building new ones programmatically. Learning Outcomes: 1. Knowledge & Understanding: By the end of the study-unit the student will be able to: - Describe how to analyse a molecular biology project using computational tools; - List computational tools available to execute genomic and proteomic analysis; - Explain the differences between local and global sequence alignment; and - Explain how to align DNA and protein sequences (to a reference) and find variants/mutations. 2. Skills: By the end of the study-unit the student will be able to: - Execute an analysis on a molecular biology project using computational tools; - Align DNA and protein sequences (to a reference) and find variants/mutations; - Evaluate whether the underlying theoretical assumptions of specific bioinformatics tools apply to the data at hand; - Use (and query) of sequence and structure databases to support findings; - Use BLAST family of tools to search for similar sequences; - Use Clustal family of tools to align multiple sequences; - Use of Galaxy platform for bioinformatics analysis; - Use of GeneCards database for gene annotation; and - Use PDB to search for protein structures. Main Text/s and any supplementary readings: Main Text: - Lesk, A. Introduction to Bioinformatics. 4th edition. Oxford: Oxford University Press. 2014. Supplementary Readings: - Orengo, C., Jones, D. and Thornton, J. Boinformatics: genes, proteins and computers. Milton Park: Garland Science. 2003. - Xiong, J. Essential Bioinformatics. Cambridge: Cambridge University Press. 2006. - Durbin, R., Eddy, S. R., Krogh, A., and Mitchison, G. Biological Sequence Analysis: Probabilistic models of proteins and nucleic acids. Cambridge: Cambridge University Press. 1998. - Parrington, J. The Deeper Genome: Why there is more to the human genome than meets the eye. Oxford: Oxford University Press. 2015. - Mount, D. Bioinformatics: Sequence and Genome Analysis. nd edition. Cold Spring Harbor Press. 2004. - Pevsner, J. Bioinformatics and Functional Genomics. 3rd edition. Wiley-Blackwell Publishers. 2015. |
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| STUDY-UNIT TYPE | Lecture, Project & Computer Lab Sessions | ||||||||
| METHOD OF ASSESSMENT |
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| LECTURER/S | Panagiotis Alexiou Byron Baron (Co-ord.) Joseph Bonello |
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The University makes every effort to ensure that the published Courses Plans, Programmes of Study and Study-Unit information are complete and up-to-date at the time of publication. The University reserves the right to make changes in case errors are detected after publication.
The availability of optional units may be subject to timetabling constraints. Units not attracting a sufficient number of registrations may be withdrawn without notice. It should be noted that all the information in the description above applies to study-units available during the academic year 2024/5. It may be subject to change in subsequent years. |
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