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2004/05 Undergraduate Module Catalogue

BIOL3000 Bioinformatics

10 creditsClass Size: 999

Module manager: Dr Alan Radford

Taught: Semester 1 (Sep to Jan), Semester 2 (Jan to Jun) View Timetable

Year running 2004/05

Pre-requisites

Some lower level biochemistry and genetics.

This module is approved as an Elective

Objectives

The objectives of this module would be that, at the end of it, students will 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

The use of DNA and protein sequence databases and analysis of such sequences: 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 include Entrez and SRS for Genbank and PDB. Database searching with FASTA and /or BLAST to identify homologues. Bibliographic searching of Medline (Pubmed), featured 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 with Dotter. Multiple alignment of related sequences using Clustal, allow a comparison of the identified motifs with the conversation of their alignment, identification of conversed residues. Phylogenetic analysis with clustal and tree display and manipulation with Treeview. Extraction of structural data from PDB and display in Rasmol. Secondary and tertiary structure with Rasmol. Using AceDB, in silico contig assembly across a gene of known function would be undertaken. This would be extended to identify its map location with respect to flanking genes. Using this sequence, human homologues would be sought. Tissue-specific expression of the human homologues would be studied using EST databases.

Teaching methods

Lectures: 5 x 1 hour; 5 x 3 hour supported cluster teaching.

Methods of assessment

Assessment is based entirely on a set of six individual assignments. The first five assignments are based on work covered in each of the five lecture/computer sessions. The sixth assignment is an essay on the area of genomics and proteomics, based on available WwW resources.

Reading list

The reading list is available from the Library website

Last updated: 13/12/2004

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