Computational genomics algorithms

Course guarantor:

Jan Holub

Lecturer:

Jan Holub

Tutor:

Jan Holub

Supervisor:

Department of Theoretical Computer Science

Synopsis:

The course deals with efficient algorithms for various tasks in bioinformatics. One fo such task is an alignment of two or more sequences. Other topic covers algorithms for individual phases of genome assembly. The course also presents compressed data structures for storing and indexing genomes and very fast pattern matching in them. Algorithms for efficient analysis and comparison of genomes.

Requirements:

The course is aimed to Ph.D. students.

Syllabus of lectures:

1. Multiple sequence alignment algorithms I - scoring systems, dynamic programming

2. Multiple sequence alignment algorithms II - heuristic algorithms - progressive and branch and bound methods

3. Read alignment algorithms

4. Genome assembly and string graphs

5. De Bruijn graphs and Eulerian walks

6. Building de Bruijn graphs

7. Representations of de Bruijn graphs

8. Scaffolding algorithms

9. Genome compression I - LZ based

10. Genome compression II - BWT based

11. Genome analysis and comparison I - space-efficient genome analysis

12. Genome analysis and comparison II - comparing genomes without alignment

13. Latest developments in computational genome processing

14. Summary of algorithms for computational genomics

Syllabus of tutorials:

Study Objective:

Students will know:

- Basics principles of algorithms for multiple sequence alignment,

- algorithmic background of genome assembly,

- data compression methods used for efficient storage and indexing genomes,

- algorithmic background of genome analysis and comparison.

Study materials:

- V. Mäkinen, D. Belazzougui, F. Cunial, A.I. Tomescu: Genome-Scale

Algorithm Design: Biological Sequence Analysis in the Era of

High-Throughput Sequencing. Cambridge University Press, 2015. ISBN:

978-1107078536

- E. Ohlebusch: Bioinformatics Algorithms: Sequence Analysis, Genome

Rearrangements, and Phylogenetic Reconstruction. Oldenbusch Verlag,

2013. ISBN: 978-3000413162

Note:

Time-table for winter semester 2024/2025:

Time-table is not available yet

Time-table for summer semester 2024/2025:

Time-table is not available yet

The course is a part of the following study plans:

• Informatics (doctoral) (compulsory elective course)
• Informatics (compulsory elective course)