BIOINF4110 Sequence Bioinformatics
| Lecturer | Prof. Dr. Daniel Huson and Anupam Gautam |
| 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 | Mondays, Wednesdays, Thursdays 8:15-10:00 |
| Exam | The exam will take place in two parts. Part 1: Dec 4th 2024, Part 2: Feb 5th 2025 |
| 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.
Script and assignments
The script and assignment sheets 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 |
|---|---|---|
| 14.10. | 1. Introduction | |
| 16.10. | 2. Pairwise sequence alignment (global, local, overlap, linear and affine gaps, linear space and banded) | Ass. 01 |
| 21.10. | continued | |
| 23.10. | 3. Multiple alignment (progressive, using ILP) | Ass. 02 |
| 28.10. AG | 4. DIAMOND protein alignment | |
| 30.10. AG | 5. Pan genome analysis | Ass. 03 |
| 04.11. | 3. continued | |
| 06.11. | 6. Phylogenetics (distance-based, max parsimony, max likelihood, Bayesian analysis) | Ass. 04 |
| 11.11. | continued | |
| 13.11. | continued | Ass. 05 |
| 18.11. AG | 7. Microbiome analysis (16S, WGS) | |
| 20.11. AG | continued | Ass. 06 |
| 25.11. | 6. continued | |
| 27.11. | 8. Suffix trees (MUMs, inexact matching, maximal repeats) | Practice exam |
| 02.12. | continued | |
04.12.24 11:15-12:45 N6, Morgenstelle | Exam part I This will cover the first part of the course, chapters 2-8.
| Ass. 07 |
| 09.12. | 9. Genome comparison (Mauve and mash)
| |
| 11.12. | continued | Ass. 08 |
| 16.12. | 10. Read mapping (Bowtie and minimap) | |
| 18.12. | continued | Ass. 09 |
| Christmas break | ||
| 08.01.25 | 11. Classic string matching. | Ass. 10 |
| 13.01.25 | 12. Sequence assembly (Velvet and miniasm) | |
| 15.01.25 | continued | Ass. 11 |
| 20.01.25 | 13. Population genetics | |
| 22.01.25 | continued | Ass. 12 |
| 27.01.25 in A301, Sand | 14. SVMs | |
29.01.25 8:15-10:00 C118a, Sand 10:15-12h, F119, Sand | Group project presentations | Practice exam |
| 03.02.25 | Exam prep. | |
05.02.25 12:15-13:45 N10, Morgenstelle | Exam part II This will cover the second half of the course, chapters 9-14.
| |
| Makeup exam | Wednesday, April 3rd, Part 1: 8-10h, Part 2: 10-12h, Date and location: To be confirmed |
How to get credit for this course
- Always participate in the weekly problem sessions and actively present your results. If you miss more than two tutorials, then you will not be allowed to take the exam.
- Assignments are set weekly and are due the following week.
- Obtain at least 50% of all points. If you obtain 70%, 80% or 90% of all possible assignment points, then you will receive bonus points toward your exam.
- Pass both parts of the exam.