|Lecturer||Prof. Dr. Daniel Huson|
Mondays, Wednesdays 10-12h. (Venue: F122, Sand 6/7)
Lectures will be held in person and also recorded and uploaded to Ilias.
Please visit Ilias to check rules on who may attend lecturers in-person.
|Assignments||Will be made available on Wednesdays and are due 7 days later on Wednesday, 10 a.m.|
A: Mondays, 8-10, online
B: Wednesdays, 8-10, F122, Sand 6/7
C: Thursdays, 8-10, F122, Sand 6/7
|Exams||Written exam in two parts. Part I will take place on Dec 15, part II will take place at the end of semester.|
|Audience||Master students bioinformatics, 9 LP|
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 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.
The following schedule is subject to change.
|20.10.21||2. Pairwise sequence alignment||Assignment 01|
|27.10.21||3. Multiple sequence alignment||Assignment 02|
|8.11.21||4. Phylogenetic trees|
|24.11.21||5. Suffix trees, MUMs and maximal repeats||Assignment 06|
|6.12.21||6. Genome comparison|
|13.12.21||7. DIAMOND protein alignment|
Exam part I - in N 10, Hörsaalzentrum Morgenstelle
This covers chapters 1-7.
8. Read mapping using the BWT or minimizers
10. Genome assembly algorithms
|19.01.22||11. RNA-seq||Assignment 11|
|24.01.22||12. Population genetics|
|26.01.22||13. Microbiome analysis||Assignment 12|
|02.02.22||14. SVMs||Practice exam|
Exam part II - time and place not yet confirmed
This covers chapters 8-14.
|Makeup exam|| |
(There will be a makeup exam for both part I and for part II of the exam. These will take place back-to-back on the same day.)
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.