2019/20 Undergraduate Module Catalogue
BLGY2201 Introduction to Bioinformatics
10 creditsClass Size: 120
Module manager: Dr Glenn McConkey
Taught: Semester 2 View Timetable
Year running 2019/20
Module replacesBIOL2201 The Human Genome - Potentials and Applications
This module is approved as a discovery module
Module summaryThis 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.
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.
- 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.
|Delivery type||Number||Length hours||Student hours|
|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
|Assessment type||Notes||% of formal assessment|
|In-course Assessment||Work covered in each of the five lecture/computer sessions (20% each)||100.00|
|Total percentage (Assessment Coursework)||100.00|
Normally resits will be assessed by the same methodology as the first attempt, unless otherwise stated
Reading listThe reading list is available from the Library website
Last updated: 25/04/2019
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