Content (Syllabus outline)
DNA sequence, protein sequence and protein structure information databases (file formats, retrieval, data analysis). Annotated sequence databases - primary sequence databases, protein sequence and structure databases (file formats, retrieval, data analysis). Sequence similarity: local vs. global, distance metrics, similarity and homology, Scoring matrices, alignment algorithms. Next generation sequencing: data, methods. Genome assembly: data, methods. Phylogeny and taxonomy: databases, phylogeny reconstruction algorithms. Whole genome analysis: databases, algorithms. Comparison of genomes, transcriptomes and proteomes of selected model bacetrial, archeal, fungal, plant and animal organsism, and humans. Gene expression analysis: technology, databases, introduction to computational approaches. Dynamics of biological process based on proteins and nucleic acids. Integrative genomics and systems biology: databases, methods. Statistically supported data analysis: continuous and discrete probability distributions, parameters and parameter estimation, populations and samples, basic concepts and logic of statistical reasoning, types of statistical tests, multiple linear and logistic regression analysis. Concepts of linear algebra (matrices, eigenvalues), derivatives and integrals.
Prerequisites
Prerequisites for admittance to final exam:
- presence at at least 80% of practicals,
- completed homework assignments,
- project presentation.