SubjectsSubjects(version: 876)
Course, academic year 2020/2021
  
Computational genomics algorithms - AP500002
Title: Computational genomics algorithms
Guaranteed by: CTU in Prague, Faculty of Information Technology (500)
Actual: from 2019
Semester: both
Points: 0
E-Credits: 0
Examination process:
Hours per week, examination: 3/0 other [hours/week]
Capacity: winter:unlimited / unknown (unknown)
summer:unknown / unknown (unknown)
Min. number of students: unlimited
Language: English
Teaching methods: full-time
Level:  
For type: doctoral
Note: you can enroll for the course in winter and in summer semester
Guarantor: Holub Jan prof. Ing. Ph.D.
Interchangeability : P500002
Annotation -
Last update: Pátková Vlasta (08.06.2018)
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: Pátková Vlasta (08.06.2018)

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: Pátková Vlasta (08.06.2018)

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: Pátková Vlasta (08.06.2018)

Online course materials

Syllabus -
Last update: Pátková Vlasta (08.06.2018)

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: Pátková Vlasta (08.06.2018)

Algorithmic thinking

Course completion requirements -
Last update: Pátková Vlasta (08.06.2018)

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

 
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