Algorithms in Bioinformatics

BIOINF4110 - Sequence Bioinformatics

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
Language English
Links Campus   Ilias


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. 

Date Topic Assignments Lecturer
 15.10. 1. Introduction   DH
 17.10. 2. Pairwise sequence alignment  Assign. 01 DH
 22.10. continued    DH
 24.10. continued Assign. 02 DH
 29.10.. 3. Multiple sequence alignment    Benjamin
31.10.. continued Assign. 03 Benjamin
  5.11. continued   DH
  7.11. 4. Phylogenetic trees Assign. 04 DH
 12.11. continued   DH
 14.11. continued Assign. 05 DH
 19.11. continued   DH
 21.11.  5. RNA-seq Assign. 06 GS
 26.11. continued   GS
 28.11. 6. Suffix trees Assign. 07 DH
  3.12. continued   DH
  5.12. continued Practice exam DH
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
  9.1. continued  Assign. 10 GS
 14.1. 11. Genome comparison   DH
 16.1. continued  Assign. 11 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)
Even student id number: A104, Sand 1
Odd number:
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.