Algorithms in Bioinformatics

BIOINF4110 Sequence Bioinformatics

Lecturer Prof. Dr. Daniel Huson
Time and place

Mondays, 10:15-12:00, Wednesdays 10:15-12h. (Venue: A301, Sand 1)

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 and Alma
Exam The exam will take place in two parts. Part 1: Dec 6?, Part 2: Feb 7?
Audience Master students Bioinformatics, Medical Informatics, Computer Science
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 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.

Schedule

The following schedule is subject to change. 

Date Topic Assignments
16.10.23 1. Introduction  
18.10.23 2. Pairwise sequence alignment (global, local, overlap, linear and affine gaps, linear space and banded) Ass. 01
23.10.23 continued  
25.10.23 3. Multiple alignment (progressive, using ILP) Ass. 02
30.10.23 continued Ass. 03
06.11.23 continued  
08.11.23 4. Phylogenetics (distance-based, max parsimony, max likelihood, Bayesian analysis) Ass. 04
13.11.23 continued  
15.11.23 continued Ass. 05
20.11.23 continued  
22.11.23 5. Suffix trees (MUMs, inexact matching, maximal repeats) Ass. 06
27.11.23 continued  
29.11.23 6. DIAMOND protein alignment Practice exam
04.12.23 10:15-11:45

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

Location: A301 (even student-id number), F122 (odd number)

 

06.12.23

7. Genome comparison (Mauve and mash) Ass. 07

11.12.23

continued  

13.12.23

8. Read mapping (Bowtie and minimap) Ass. 08
18.12.23 continued  

20.12.23

9. Classic string matching Ass. 09

 

Christmas break  
08.01.24  10. Sequence assembly (Velvet and miniasm)  
10.01.24 continued Ass. 10
15.01.24 11. Microbiome analysis (16S, WGS)  
17.01.24 continued Ass. 11
22.01.24 What do bioinformaticans actually do? Presentation and discussion with bioinformaticans working at  GeCaT GmbH  
24.01.24 12. Population genetics Practice exam
29.01.24 13. SVMs  

31.01.24  8:15-12:00

Group project presentations

 
05.02.24 10:15-11:45

Exam part II This will cover the second half of the course, chapters 7-13.

Location: A301 (even student-id number), F122 (odd number)

 

 

 

 
Makeup exam

Wednesday, April 3rd, TBA

 

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.
  • Pass both parts of the exam.