Algorithms in Bioinformatics

BIOINF4110 Sequence Bioinformatics

Lecturers Prof. Dr. Daniel Huson, Timo Lucas, Dr. Monika Zeller and Wenhuan Zeng
Lectures 

Prerecorded lecturers will be made available Mondays at 10am via Ilias.

The lecturer is available for questions and discussions every Wednesday at 10:15 (via Zoom).

Assignments

Assignments will be made available Mondays at 10am via Ilias. Solutions are due 8 days later by Tuesday 8am. 

Tutorials

Weekly tutorials will take place Mondays 10:15-11:45 (groups A and C) and Thursdays 10:15-11:45 (group B) via Zoom, starting 9-Nov. Participation is mandatory.

Exams Written exam, in person, time and place to be announced.
Audience Master students bioinformatics, 9 LP
Language English
Links Alma Ilias

Contents

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.

Schedule

The following schedule is subject to change. 

Date Topic Assignments
2.11.20 1. Introduction  
  2. Pairwise sequence alignment  Assign. 01
9.11.20 continued   
  3. Multiple sequence alignment  Assign. 02
16.11.20 continued  
  4. Phylogenetic trees Assign. 03
23.11.20 continued  
  continued Assign. 04
30.11.20 continued  
  5. Classic string matching Assign. 05
7.12.20 6. Suffix trees, MUMs and maximal repeats  
  continued Assign. 06
14.12.20 continued  
  7. Read mapping using the BWT or minimizers Assign. 07
21.12.20 continued  
  8. Genome assembly algorithms Assign. 08
11.1.21 continued  
  continued Assign. 09
18.1.21 9. Genome comparison  
  continued  Assign. 10
25.1.21 10. RNA-seq  
  11.  Population genetics  Assign. 11
1.2.21 12. SVMs  
  13. Beyond BLAST: DIAMOND  Assign. 12
8.2.21 14. Microbiome analysis  
  continued  Assign. 13
15.2.21 continued  
  continued Practice exam

24.2.21 

Exam 17:00-19:30h in N10, Morgenstelle  
     
     
 

There will be a makeup exam on March 31 (date not yet confirmed).

 

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 the exam.