|Lecturers||Prof. Dr. Daniel Huson and Dr. Gabriele Schweikert|
|Teaching assistants||Xi Chen and Sascha Patz|
|Lectures||Mondays, 10:15-12:00, Hörsaal 2, Sand 6/7 |
Wednesdays, 10:15-12:00, A 104, Sand 14
|Problem sessions||A) Sascha Patz, Thursdays 8-10, Hörsaal 2, Sand 6/7 |
B) Xi Chen, Mondays 8-10, Hörsaal 2, Sand 6/7
|Target audience||MSc students in bioinformatics|
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.
The following schedule is subject to change.
|17.10.||2. Pairwise sequence alignment||Assign. 01||DH|
|29.10..||3. Multiple sequence alignment||Benjamin |
|31.10..||continued||Assign. 03||Benjamin |
|7.11.||4. Phylogenetic trees||Assign. 04||DH|
|21.11.||5. RNA-seq||Assign. 06||GS|
|28.11.||6. Suffix trees||Assign. 07||DH|
| 10.12. |
Hörsaal 1, Sand 6/7
|First part of exam (chapters 1-6)|
|12.12.||7. Sequence assembly||Assign. 08||DH|
|17.12.||8. Read mapping||DH|
|19.12.||9. Chromatin / TF binding/ Histone modifications||(Assign. 09)||GS|
|7.1.||10. DNA methylation||GS|
|14.1.||11. Genome comparison||DH|
|21.1.||12. Population genetics||DH|
|23.1.||13. SVMs||Assign. 12||DH|
|28.1.||14. Beyond BLAST: DIAMOND||DH|
|30.1||15. Classic string matching||Practice exam||DH|
|4.2.||Free for exam preparation |
(If you have questions, please arrange to meet with your tutor between 10 and 12 o'clock)
| 6.2. |
Even student id number: A104, Sand 1
C118, Sand 14
|Second part of exam (chapters 7-15)|
If you miss or fail part (1) of the exam, then you can take a makeup exam for part 1 on Monday, Jan 7th 8:15-10 in A301, Sand 14.
If you miss or fail part (2) of the exam, then you can take a makeup exam for part 2 on Friday, March 29th 8:15-10 in Hörsaal 1, Sand 6/7.