Introduction to Bioinformatics

• explain how the information in biological macromolecules, such as DNA and protein can be represented in an electronical format.
• explain how DNA and protein sequences from related organisms are influenced by a common evolutionary history.
• search for sequence and structure data from the publicly available databases, such as GenBank, UniProt and PDB.
• visualize protein 3D structure using computer software.
• generate and critically evaluate DNA and peptide alignments.
• query sequence databases using alignment based methods (BLAST) and critically evaluate the results
• predict the most probable biological function of a novel gene or protein product by comparison to already characterized genes/proteins.
• use programs to generate multiple sequence alignments of sets of related sequences.
• generate phylogenetic trees from multiple alignments.
• generate and interpret visualizations of the information content of sets of related sequences (“logo plots”).

Evolution at the DNA level. Taxonomy. Practical use of taxonomy databases.

Biological information. Information content in biological macromolecules. DNA sequencing – including error sources. DNA sequences in electronical format. How to use the GenBank database.

Protein sequences. Protein structure levels. Protein sequences in electronical format. Sources of protein sequences (direct sequencing and computer based translation). How to use the UniProt database.

Protein structure. How protein structures are determined. Quality of protein structure data. How to use the PDB database. Computer based visualization of protein structure.

Pairwise alignment. Alignment scores, gaps, substitution matrices. Global and local alignment.

BLAST. How to use BLAST for searching sequence databases. Critical evaluation of results. Iterative BLAST.

Multiple alignments. The use of heuristic methods due to data complexity.

Generation and interpretation of phylogenetic trees from multiple alignments. The NJ algorithm for tree construction. Rooted versus unrooted trees.

Weight-matrix based methods. How to search using weight-matrices. Generation and interpretation of LOGO plots.

27002/27008, Basic understanding of biological processes used in the industry. Knowledge of cell structure, their biological functions, biochemical and molecular biological processes together with biotechnological processes

Lectures and computer exercises