Bioinformatics & Genome Analysis
Contents
Objective: To describe methods, problems and results in the analysis of the structural information in protein and DNA sequences.
The large growth in known DNA sequences (and proteins) and of known structures makes the analysis of these data an important discipline.
1. Introduction to the field: 1 week
What are the data and the main problems.
2. Sequence Comparison (Alignment): 2 weeks
Pairwise comparison (alignment). Comparison of many sequences (Multiple Alignment). Database search. Statistical significanse of sequence similarities. Weight matrices for amino acids.
3. Structure prediction: 4 weeks
RNA secondary structure prediction - energy minimization (basepairing maximization) and coupled substitutions. The prediction of protein secondary structure. The Protein Foldning Problem: Teoretical models and empirical results. Homology modelling: Given two (or more) homologous sequences, where only one of the structures of the sequences is known, what can then be said about the structure of the other proteins? How closely related must the sequences be for homology modelling to be used? If the molecular evolution of a set of homologous proteins has been reconstructed, what can then be said about their structure? Molecular Dynamics: Computer simulations of macromolecules movement and interactions.
3. Structure comparison: 2 weeks
Comparison of tertiary protein structures. Comparison of RNA-secondary structures. Combined structure-prediction and structure comparison. Docking: Does two given structures fit into each other? Does a sequence fit a structure (Threading)?
4. Genome projects: 4 weeks
Homo sapiens, C. elegans, yeast,.. Comparison of Genomes. Searching for genes in genomic sequences. Searching for regulatory sequences in genomic sequences. Reconstruction of Ancient Metabolic Pathways. Functionel Classifikation of genes. The search for disease genes and for genes responsible for quantitiative traits (QTLs).
Maximum number of pupils: 24
Evaluation
Participation in the course - (passed/not passed).
ECTS-credits
10
Semester
Fall 1999
The course will only be offered every second year.
Students, attending Bioinformatics & Genome Analysis, can choose to write an essay on a relevant subject within this field - possibly involving analysis of a specific dataset. The student will be assisted in finding subject and literature by the teacher.
Evaluation
Evaluation after the 13-scale
ECTS-credits
5
Semester
Fall 1999