Homepage of the course
http://www.daimi.au.dk/~schauser/bioinformatics_E03
Credits
5 ECTS
Aim
The large increase of DNA and protein sequences and protein structures make the analysis of these data to an important discipline. The course identifies and describes problems, methods and results in the analysis of protein- and DNA-sequences.
Contents
The course is focused on methods. We will discuss problems that arise when analysing biological sequences and structures. Focus is on the development of models in order to solve a problem. Basic algorithms will be described. The course takes a practical approach: there will be introduced a number of computational tools that can solve problems with high efficiency.
1. Introduction to the field. What kind of data is available and what are the main problems in their analysis.
2. Sequence alignment. Pair wise alignment. Multiple alignments. Statistical significance of sequence similarity. Substitution matrices for amino acids. Analysis of protein domains.
3. Structure prediction. Prediction of RNA secondary structure: energy minimization (base pair maximization) and covariant substitutions.
4. Database searches. Databases, Blast, Fasta heuristics.
Term
1st quarter
Prerequisites
Passed 1st year courses in Molecular Biology
Type of classes
21 lectures
21 computer exercises
Type of evaluation and aids
Project-thesis evaluated according to the 13 point scale with intern examiner
Educational materials
Textbook: BIOINFORMATICS – Sequence and Genome Analysis
Author: D. W. Mount
Publishing house: Cold Spring Harbor Laboratory Press
ISBN No: 0-87969-608-7
Supplementary material
None
Responsible teacher
Name: Leif Schauser
Office address: Building 90, office 121
Phone no: +45 8942 3239
E-mail: schauser@daimi.au.dk
Other teachers
Christian Storm, Mikkel Schierup and Søren Thierup
Max participants
No limit
Language
Material: English
Spoken language: Danish/English