BIOINF4110 Sequence Bioinformatics
| Lecturers | Prof. Dr. Daniel Huson, Timo Lucas, Dr. Monika Zeller and Wenhuan Zeng |
| Lectures | Prerecorded lecturers will be made available Mondays at 10am via Ilias. The lecturer is available for questions and discussions every Wednesday at 10:15 (via Zoom). |
| Assignments | Assignments will be made available Mondays at 10am via Ilias. Solutions are due 8 days later by Tuesday 8am. |
| Tutorials | Weekly tutorials will take place Mondays 10:15-11:45 (groups A and C) and Thursdays 10:15-11:45 (group B) via Zoom, starting 9-Nov. Participation is mandatory. |
| Exams | Written exam, in person, time and place to be announced. |
| Audience | Master students bioinformatics, 9 LP |
| 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 some of the most fundamental algorithms used in bioinformatics. Programming assignments are to be solved in Python. 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 available here: Ilias
Also, please upload your solutions to the assignment sheets there.
Schedule
The following schedule is subject to change.
| Date | Topic | Assignments |
|---|---|---|
| 2.11.20 | 1. Introduction | |
| 2. Pairwise sequence alignment | Assign. 01 | |
| 9.11.20 | continued | |
| 3. Multiple sequence alignment | Assign. 02 | |
| 16.11.20 | continued | |
| 4. Phylogenetic trees | Assign. 03 | |
| 23.11.20 | continued | |
| continued | Assign. 04 | |
| 30.11.20 | continued | |
continued | Assign. 05 | |
| 7.12.20 | 5. Classic string matching | |
| 6. Suffix trees, MUMs and maximal repeats | Assign. 06 | |
| 14.12.20 | continued | |
| continued | Assign. 07 | |
| 21.12.20 | 7. Genome comparison | |
| continued | Assign. 08 | |
| 11.1.21 | 8. Read mapping using the BWT or minimizers | |
| continued | Assign. 09 | |
| 18.1.21 | 9. DIAMOND protein alignment | |
continued | Assign. 10 | |
| 25.1.21 | 10. Genome assembly algorithms | |
| continued | Assign. 11 | |
| 1.2.21 | 11. RNA-seq | |
| 12. Population genetics | Assign. 12 | |
| 8.2.21 | 13. Microbiome analysis | |
| continued | Assign. 13 | |
| 15.2.21 | 14. SVMs | |
| continued | Practice exam | |
24.2.21 | Exam on 24.2.21,12:15-14h in N6, Morgenstelle | |
| 31.3.21 | Makeup exam on 31.3.21, 10:15-12h in N02, Morgenstelle (You may participate in the makeup exam only if (a) you attained at leat 50% of all assignment points, and (b) you missed or failed the exam on 24.2.2021.) | |
| |
Due to the pandemic, there will be a second makeup exam on September 28th, 14:15-16h. Meeting point: C310a, Sand 14. Please send an email to Prof. Daniel Huson if you intend to participate in this exam, and indicate whether you will adhere to 3G rules or not.
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. (Due to the pandemic, we will count these points toward your exam even if you don't participate on the first date.)
- Pass the exam. (No need to register for the first exam if you intend to take part in a later exam.)