2024/25 Undergraduate Module Catalogue

BLGY2201 Introduction to Bioinformatics

10 creditsClass Size: 98

Module manager: Dr Glenn McConkey
Email: g.a.mcconkey@leeds.ac.uk

Taught: Semester 2 (Jan to Jun) View Timetable

Year running 2024/25

This module is approved as a discovery module

Module summary

This module will enable students to access publicly available biological databases of genome, sequence, structure, physical mapping and bibliographic, search and query them, extract data from different databases, and analyse and display results using appropriate software. Wherever possible WWW-accessible resources are used, to ensure maximum transferability of the knowledge gained. It is not the objective to teach relevant programming skills but to teach how to use available resources.

Objectives

This independently-driven module introduces students to the basic concepts of bioinformatics and illustrates the application of bioinformatics to many biological questions. The module shows how genomic data is stored and accessed to learn about any characterised gene or protein and how it links to resources on research. The approaches to modern phylogenetics are introduced and how bioinformatics is applied to drug discovery.

Learning outcomes
On completion of this module, students should be able to:
- access publicly available biological databases of genome, sequence, structure, physical mapping and bibliographic, search and query them, extract data from different databases, and analyse and display results using appropriate software.

Wherever possible WWW-accessible resources are used, to ensure maximum transferability of the knowledge gained. It is not the objective to teach relevant programming skills but to teach how to use available resources.

Syllabus

- Using DNA and protein sequence databases and analysing sequences, with particular reference to the Human Genome Project: organism-specific genome databases, OMIM (for human genetic diseases), Genbank (for DNA and protein sequences), Swissprot (for protein sequences) and PDB (for molecular structures). Query and extraction software.
- Database searching with FASTA and/or BLAST to identify homologues.
- Bibliographic searching of Medline (Pubmed), features analysis via Prosite.
- Analysis of an unknown DNA sequence to identify coding regions, promoter, intron splice sites, lariat sequences, poly-A-sites.
- PCR primer design.
- Secondary structure prediction.
- Pairwise DNA and protein sequence comparison.
- Multiple alignment of related sequences using Clustal, allowing comparison of identified motifs, identifying conserved residues.
- Phylogenetic analysis with Clustal and tree display with Treeview.
- Extraction of structural data from PDB, display in Rasmol.
- Secondary and tertiary structure with Rasmol.
- Using AceDB, in silico contig assembly across a gene of known function, identifying map location, finding human homologues.
- Tissue-specific expression of human homologues using EST databases.

Teaching methods

Delivery type	Number	Length hours	Student hours
Lecture	5	1.00	5.00
Practical	5	3.00	15.00
Private study hours			80.00
Total Contact hours			20.00
Total hours (100hr per 10 credits)			100.00

Private study

- 20 hours: reading (4 hours per lecture)
- 60 hours: practical exercises.

Opportunities for Formative Feedback

- Each week for five weeks the class undertakes an exercise and an assignment.
- The exercise is handed in at the end of the three-hour session and is returned marked the following week.
- The assignment is submitted a week later and is returned as soon as possible.

Methods of assessment

Coursework

Assessment type	Notes	% of formal assessment
Practical Report	(Single report covering 2 practicals)	50.00
Practical Report	(Single report covering 2 practicals)	50.00
Total percentage (Assessment Coursework)		100.00

Normally resits will be assessed by the same methodology as the first attempt, unless otherwise stated

Reading list

The reading list is available from the Library website

Last updated: 29/04/2024 16:11:53

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