Syllabus academic year 2010/2011
(Created 2010-07-25.)
BIOINFORMATICSKBK075
Credits: 7,5. Grading scale: TH. Cycle: A (Second Cycle). Main field: Technology. Language of instruction: The course will be given in English on demand. Alternative for: MBIO1. Optional for: B4mb, B4pt. Course coordinator: Project researcher Peter Olsson, Peter.Olsson@tbiokem.lth.se, Pure and Applied Biochemistry. Prerequisites: KBK041 Gentechnology. Assessment: Problem orientated individually written home exam. Degree is given on the home exam result. Passed report from computer exercises. Home page: http://www.tbiokem.lth.se.

Aim
The course aims at giving a theoretical knowledge in bioinformatics and its potentials. The aim is also to give practical experience in searching bioinformatics databases and to use bioinformatics software.

Knowledge and understanding
For a passing grade the student must

Skills and abilities
For a passing grade the student must

Judgement and approach
For a passing grade the student must

Contents
The course comprises knowledge about bioinformatics databases, as well as software that searches such databases. Additionally, the course comprises basic knowledge about software and algorithms that can predict nucleotide or amino acid sequence's biochemical or molecular biology properties and functions. Conceptions such as FASTA format, BLAST, archival & curated database, accession number, cross reference, data base field, Boolean qualifiers, In silico, alignment, algorithm, Hidden Markov Model, Neural Networks, cluster, phylogenetic analysis, phenetic & cladistics approaches, bootstrapping, gap penalties, substitution matrices, homology modelling, threading and Ab Initio modelling are explained. An overview about systems biology and synthetic biology are given.

Examples on practical exercises are: database searching (both search using words and searching for sequences matching a known sequence) as well as interpretation of search results, phylogenetic evaluation of the probability that a dentist has infected his patients with HIV, theoretical development of a PCR method that could determine the gender of a human DNA sample, and exercises in protein modelling.

Literature
Arthur M. Lesk Introduction to Bioinformatics. Oxford University Press,2005, ISBN 0 19 9277877
Compendium: Exercises for Bioinformatics