10 ECTS, spring
Aim
To describe problems, methods and results in the analysis of structural information of protein- and DNA-sequences.
Background
The large increase of identfied DNA (and protein) sequences and structures make the analysis of these data to an important disciplin.
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 introduces a number of computational tools that can solve problems with high efficiency.
1.Introduction to the field.
What kind of data are availible and what are the main problems in their analysis.
2.Sequence alignment
Pairwise alignment. Multiple alignment. Database searches. Statistical significance of sequence similarity. Substitution matrices for aminoacids.
3.Structur prediction.
Prediction of RNA secondary structure: energy minimization (basepair maximization) and covariant substituions. Prediciton of the secondary structure of proteins. Proteinfolding: theortical models and empirical results. Assesment of the quality of structurepredictions: CASP- symposia.
4.Genefinding: What biological signals can be used in the construction of a statistical model to the prediciton of genestrucure? How can one validate the results?
5.Comarison of structures:
Comprison of 3-dimensional proteinstructures. Combined structurepredictions and comparison. Does a sequence fit to a given structure?
6.Microarray data analysis.
Dataminig tools, clustering, reconstruction of regulatory pathways. Estimating the function of unknown genes.
7.Genome projects.
Whole genome assembly. Comparison of genomes. Searches for genes in genomic sequences. Serches for regulatory sequencs, Reconstruction of metabolic pathways. Functional classification of genes.
Form
Weekly for 11 weeks: 3 hours lectures and 3 hours computer exercises.
Teachers
Leif Schauser, Christian Storm og Mikkel Schierup from Bioinformatics Research Center (BiRC).
Term
Spring 2003
Literature
David Mount: Bioinformatics: Sequence and genome analysis, original literature.
Eksamination
Oral examination, graded.