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  
 

continued

Assign. 05
7.12.20 5. Classic string matching  
  6. Suffix trees, MUMs and maximal repeats Assign. 06
14.12.20 continued  
  continued Assign. 07
21.12.20 7. Genome comparison  
  continued Assign. 08
11.1.21 8. Read mapping using the BWT or minimizers  
  continued Assign. 09
18.1.21 9. DIAMOND protein alignment  
 

continued

 Assign. 10
25.1.21 10. Genome assembly algorithms  
  continued  Assign. 11
1.2.21 11.  RNA-seq  
  12. Population genetics  Assign. 12
8.2.21 13. Microbiome analysis  
  continued  Assign. 13
15.2.21 14. SVMs  
  continued Practice exam

24.2.21 

Exam on 24.2.21,12:15-14h in N6, Morgenstelle  
31.3.21

Makeup exam on 31.3.21, 10:15-12h in N02, Morgenstelle

(You may participate in the makeup exam only if (a) you attained at leat 50% of all assignment points,

and (b) you missed or failed the exam on 24.2.2021.)

 
     
 

Due to the pandemic, there will be a second makeup exam on September 28th.

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. (Due to the pandemic, we will count these points toward your exam even if you don't participate on the first date.)
  • Pass the exam. (No need to register for the first exam if you intend to take part in a later exam.)