Biocomputer Science 1400-216BINF

1. Introduction to the Unix environment, command line usage (bash shell), SSH protocol, and an introduction to working on computational clusters.
2. Introduction to bioinformatics, molecular biology and biotechnology databases – overview and applications. Searching databases using keywords and applying logical operators in queries.
3. Comparison of two nucleotide and amino acid sequences. Searching nucleotide and amino acid sequence databases using sequences as queries.
4. Multiple sequence alignment. Analysis of protein families, family representation, and database searches using sequence profiles.
5. Sequence motifs related to function. Protein family motifs, cell compartment targeting signals, gene expression control sequences. Hidden Markov models and their applications in bioinformatics.
6. Differentiating between coding and non-coding DNA sequences (ab initio and homology-based methods).
7. Fundamentals of molecular evolution and constructing phylogenetic trees.
8. Spatial structure databases of macromolecules. Molecular graphics, principles of biopolymer structure visualization.
9. Modeling globular protein structures and model evaluation.
10. Independent solution of a sample complex problem (project).
11. Latest achievements in bioinformatics.