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410495-HS2023-0-Bioinformatics Algorithms





Root number 410495
Semester HS2023
Type of course Lecture
Allocation to subject Bioinformatics
Type of exam Written exam
Title Bioinformatics Algorithms
Description This course constitutes an introduction to the theory of algorithms, with a strong focus on applications in Bioinformatics. In this course I will try to find a good balance between theory, classical algorithms in mathematics and informatics, and their application in biology. Students should have basic knowledge of molecular biology, programming, and mathematics. The main format of the course will be lectures but occasionally we will do some exercises in R during the course. Please bring a laptop computer with R and RStudio installed and running.

The course will cover the following areas (subject to change throughout the semester):

1) Introduction to Algorithms
- Example: Fibonacci numbers
- Complexity and Big-O notation
2) Sequence Alignment
- Exhaustive search algorithms
- Dynamic Programming
- Local/Global alignments
- BLAST
- algorithms for NGS data
3) Motig finding problems
- Search trees
4) Greedy Algorithms
- Genome rearrangements/Towers of Hanoi
- Permutations
- Sorting by reversals
5) Graph algorithms
- Introduction to Graphs
- From genetics to graphs
- Shortest superstring problem, DNA sequencing
- Seven Bridges of Königsberg
- De Bruijn Graphs
5) Support Vector Machines
6) Phylogenetics
- Parsimony
- Neighborhood joining algorithm
- Likelihood of trees
ILIAS-Link (Learning resource for course) Registrations are transmitted from CTS to ILIAS (no admission in ILIAS possible). ILIAS
Link to another web site
Lecturers Dr. Stephan Peischl, Teaching Staff, Faculty of Humanities ✉
ECTS 3
Recognition as optional course possible Yes
Grading 1 to 6
 
Dates Monday 09:15-11:00 Weekly
Monday 15/1/2024 09:15-11:00
Monday 3/6/2024 09:15-11:00
 
Rooms Seminarraum 115, Hauptgebäude H4
External rooms Room 205, main building (Hochschulstrasse 4)
 
Students please consult the detailed view for complete information on dates, rooms and planned podcasts.