1. Explain some of the issues and challenges in contemporary bioinformatics
2. Evaluate bioinformatics algortihms
3. Design algorithms solving sequence assembly problems
4. Compare and evalute methods for sequence alignment
5. Design algorithms for building phylogenetics trees
6. Analyze data from biological databases
7. Design index structures based on suffix trees and suffix arrays

Lectures in the classroom

Team work on the implementation of a method.

1. Protein, RNA and DNA, Bioinformatics databases, Data formats
2. Biological sequences and structures, Dynamic programming algorithms, Project
3. Dynamic programming algorithms, Project
4. Suffix trees, Project
5. Suffix trees, Project
6. Suffix arrays, Project
7. Suffix arrays, FM index, Project
8. Midterm exam
9. Multiple sequence alignment, Database search, Basic Local Alignment Search Tool (BLAST) algorithm
10. Alignment, Substitution model, Project
11. Tree building, Tree evaluation, Project
12. Sequencing methods, Read mapping, Project
13. De novo assembly, Overlap-Layout-Consensus, Project
14. String graph, De Bruijn graph, Project
15. Final exam