|Lecturer||Prof. Dr. Daniel Huson|
Mondays, 10.00-11:45, Wednesdays 10-:15-12h. (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
|10.01.22||9. Genome assembly algorithms|
|17.01.22||10. Microbiome analysis|
|26.01.22||12. Population genetics||Assignment 12|
|02.02.22||Group project presentations (Online via Zoom)||Practice exam|
|07.02.22||Zoom session to discuss questions regarding the exam.|
Exam part II - in N10, Hörsaalzentrum Morgenstelle
This covers chapters 8-13.
|Makeup exam|| |
Wednesday, March 30th, F119, Sand 6/7, Part I: 9:15-11h, Part II: 11:15-13h
Due to the pandemic, there will be a second makeup exam on September 28th, 14:15-15:45h (part 1) and 16:00-17:30h (part 2). Location: F119, Sand 6/7. Please send an email to Prof. Daniel Huson if you intend to participate in this exam.
(You can try each part of the exam at most twice. Once you have passed a part of the exam, you may not retake that part.)
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.