BIOINF4110 Sequence Bioinformatics
| Lecturer | Prof. Dr. Daniel Huson and lab members |
| Time and place | Mondays, 10:15-12:00, Wednesdays 10:15-12h. (Venue: F119, Sand 6/7) Lectures will be held in person and also recorded and uploaded to Ilias. |
| Register | Via Ilias. |
| Assignments | Will be made available on Wednesdays and are due 7 days later on Wednesday, 10 a.m. |
| Tutorials | Tutorial A: Mondays 8-10h (C215), B: Mondays 8-10h (A302), C: Wednesdays 8-10h (C215) and D: Wednesdays 8-10h (A302) |
| Exam | The exam will take place in two parts. Part 1: Nov 30, 2026 Part 2: Feb 1 2027 |
| Audience | Master students: Bioinformatics, Medical Informatics, Computer Science |
| Language | English |
| Links | Alma Ilias |
Contents
Sequence Bioinformatics focuses on concepts, data-structures and algorithms for sequence analysis. Our goal is to teach you to understand, to be able to implement and to apply the most important algorithms used in bioinformatics. Programming assignments are to be solved in Java. Students will be assigned projects in which the goal will be to address a biological problem using methods discussed in the lectures.
Some contents of this lecture were already taught in "Grundlagen der Bioinformatik". While we try avoid overlap with that bachelor level course, some content is so fundamental that we cannot completely avoid some repetition of earlier material. This is for the benefit of students that do not have a BSc in bioinformatics.
Book and assignments
This lecture is based on a draft of an upcoming book called “Sequence Bioinformatics” by Daniel Huson. Videos, slides, draft book chapters and assignments will be made available via Ilias. Also, please upload your solutions to the assignment sheets there.
Schedule
The following schedule is subject to change.
| Date | Topic | Assignments |
|---|---|---|
| 12.10.26 | 1. Introduction (Lecturer: Dr. Anupam Gautam) | |
| 14.10. | 2. Pairwise sequence alignment (global, local, overlap, linear and affine gaps, linear space and banded) (Lecturer: Dr. Anupam Gautam) | Ass. 01 |
| 19.10. | continued | |
| 21.10. | 3. Multiple sequence alignment | Ass. 02 |
| 26.10. | continued | |
| 28.10. | 4. Phylogenetics | Ass. 03 |
| 02.11. | continued | |
| 04.11. | continued | Ass. 04 |
| 09.11. | continued | |
| 11.11. | continued | Ass. 05 |
| 16.11. | 5. Suffix arrays and suffix trees | |
| 18.11. | continued | Ass. 06 |
| 23.11. | 6. Read mapping | |
| 25.11. | continued | Practice exam |
| 30.11. | Exam part I This will cover the first part of the course, chapters 2-6. Time and venue: 10-12h, Hörsaal N10, Morgenstelle | |
| 02.12. | 7. Sequence assembly | Ass. 07 |
| 07.12. | continued | |
| 09.12. | 8. Genome comparison | Ass. 08 |
| 14.12. | continued | |
| 16.12. | 9. Pangenomes | Ass. 09 |
| 18.12. | 10. DIAMOND protein alignment | |
| Christmas break | ||
| 11.01.27 | 11. Microbial community profiling | Ass. 10 |
| 13.01.27 | 12. Metagenome analysis | |
| 18.01.27 | 13. Statistical methods | 9 |
| 14. Pangenomes | ||
| 25.01.27 | 15. Population genetics | Ass. 12 |
| 27.01.27 | Group project presentations | |
| 01.02.27 | Exam part II: This will cover the second half of the course, chapters 7-13. Time and venue: Hörsaal N10 (student id number not divisible by 3) and N11 (id number divisible by 3), Morgenstelle | Practice exam |
| Makeup exam | 31-March 2027. Part 1, 8-10h, Part 2: 10-12h, Venu: TBA |
How to get credit for this course
- Attend and actively participate in the weekly mandatory tutorials.
- Work on the weekly assignments and complete at least 50%.
- There will be weekly quizzes in the tutorials on material covered by the assignments. You must pass 50% of the quizzes to qualify for the exam.
- Pass both parts of the exam.