Algorithms in Bioinformatics

BIOINF4110 Sequence Bioinformatics

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
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 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
18.10.21 1. Introduction  
20.10.21 2. Pairwise sequence alignment  Assignment 01
25.10.21 continued   
27.10.21 3. Multiple sequence alignment  Assignment 02
03.11.21 continued Assignment 03
8.11.21 4. Phylogenetic trees  
10.11.21 continued Assignment 04
15.11.21 continued  
17.11.21 continued Assignment 05


24.11.21 5. Suffix trees, MUMs and maximal repeats Assignment 06
29.11.21 continued  
01.12.21 continued Assignment 07
6.12.21 6. Genome comparison  
8.12.21 continued Practice exam
13.12.21 7. DIAMOND protein alignment  



Exam part I -     in N 10, Hörsaalzentrum Morgenstelle

This covers chapters 1-7.

Assignment 08

8. Read mapping using the BWT or minimizers

22.12.21 continued Assignment 09
10.01.22 9. Genome assembly algorithms  


Assignment 10
17.01.22 10. Microbiome analysis  
19.01.22 continued Assignment 11
24.01.22 11. SVMs  
26.01.22 12. Population genetics Assignment 12
31.01.22 13. RNA-seq  
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). LocationF119, 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.