SubjectsSubjects(version: 895)
Course, academic year 2021/2022
  
Computational genomics algorithms - P500002
Title: Algoritmy výpočetní genomiky
Guaranteed by: CTU in Prague, Faculty of Information Technology (500)
Actual: from 2020
Semester: summer
Points: summer s.:0
E-Credits: summer s.:0
Examination process: summer s.:
Hours per week, examination: summer s.:3/0 other [hours/week]
Capacity: unknown / unknown (unknown)
Min. number of students: unlimited
Language: Czech
Teaching methods: full-time
Level:  
For type: doctoral
Note: course is intended for doctoral students only
can be fulfilled in the future
Guarantor: Holub Jan prof. Ing. Ph.D.
Is interchangeable with: AP500002
Annotation -
Last update: Svozil Daniel prof. Mgr. Ph.D. (23.05.2018)
The course deals with efficient algorithms for various tasks in bioinformatics. One fo such task is an alingment of two or more sequences. Other topic covers algorithms for individual phases of genome aseembly. 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.
Aim of the course -
Last update: Svozil Daniel prof. Mgr. Ph.D. (23.05.2018)

Students will know:

  • Basics principles of algorithms for multiple sequence alignment,
  • algorithmic background of genome assebmly,
  • data compression methods used for efficient storage and indexing genomes,
  • algorithmic background of genome analysis and comparison.

Literature -
Last update: Svozil Daniel prof. Mgr. Ph.D. (23.05.2018)

R: 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

R: E. Ohlebusch: Bioinformatics Algorithms: Sequence Analysis, Genome Rearrangements, and Phylogenetic Reconstruction. Oldenbusch Verlag, 2013. ISBN: 978-3000413162

Learning resources -
Last update: Svozil Daniel prof. Mgr. Ph.D. (23.05.2018)

Online course materials

Syllabus -
Last update: Svozil Daniel prof. Mgr. Ph.D. (23.05.2018)

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

2. Muliple 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

Registration requirements -
Last update: Svozil Daniel prof. Mgr. Ph.D. (23.05.2018)

Algorithmic thinking

Course completion requirements -
Last update: Svozil Daniel prof. Mgr. Ph.D. (23.05.2018)

The exam is composed of the written test and the oral exam.

 
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