Algorithms in Bioinformatics

BIOINF4110 Sequence Bioinformatics

Lecturer Prof. Dr. Daniel Huson
Time and place

Mondays, 10:15-12:00, Wednesdays 10:15-12h. (Venue: C 215, Sand 14)

Lectures will be held in person and also recorded and uploaded to Ilias.

Register Via Ilias.
Assignments Will be made available on Wednesdays and are due 7 days later on Wednesday, 10 a.m.
Tutorials See Ilias..
Exam The exam will take place in two parts. Part 1: Dec 5, Part 2: January 30
Audience Master students Bioinformatics, Medical Informatics, Computer Science
Language English
Links Alma 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 the most important algorithms used in bioinformatics. Programming assignments are to be solved in Java. 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 made available via Ilias. Also, please upload your solutions to the assignment sheets there.

Java additional support

In the first three weeks of semester, we will offer additional tutorials that will give a very basic introduction to working with Java. These will take place Fridays 8-10h via Zoom.



The following schedule is subject to change. 

Date Topic Assignments
17.10.22 1. Introduction  
19.10.22 2. Pairwise sequence alignment (global, local, overlap, linear and affine gaps, linear space and banded) Ass. 01
24.10.22 continued  
26.10.22 3. Multiple alignment (progressive, using ILP) Ass. 02
31.10.22 continued  
02.11.22 4. Phylogenetics (distance-based, max parsimony, max likelihood, Bayesian analysis) Ass. 03
07.11.22 continued  
09.11.22 continued Ass. 04
14.11.22 continued  
16.11.22 5. Suffix trees (MUMs, inexact matching, maximal repeats) Ass. 05
21.11.22 continued  
23.11.22 continued Ass. 06
28.11.22 6. Genome comparison (Mauve and mash)  
30.11.21 continued Practice exam



Exam part I This will cover the first part of the course, chapters 2-6.

Members of Tutorial A in C215, Sand 14,  members of tutorials B and C: F119, Sand 6/7



7. Read mapping (Bowtie and minimap) Ass. 07


14.12.22 8. DIAMOND protein alignment Ass. 08

19.12.22 No in-person lecture

- Lecture video on Ilias

- Tutorials via Zoom

9. Sequence assembly (Velvet and miniasm)  
21.12.22 No in-person lecture

- Lecture video on Ilias

- Tutorials via Zoom

continued Ass. 09
  Christmas break  
09.01.23 10. Microbiome analysis (16S, WGS)  
11.01.23 continued Ass. 10
16.01.22 11. SVMs  
18.01.23 What do bioinformaticans actually do? Visit to CeGaT GmbH, Paul-Ehrlich-Straße 23. Ass. 11
23.01.23 12. Population genetics  
25.01.23 9:15-12:00 Group project presentations Practice exam



Exam part II This will cover the second half of the course, chapters 7-12.

Members of Tutorial A in C215, Sand 14,  members of tutorials B and C: F119, Sand 6/7



Makeup exam

Wednesday, March 29th, Part I: 9:15-10:45h, Part II: 11:15-12:45h, C215, Sand 14


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.