Algorithms in Bioinformatics

BIOINF4110 Sequence Bioinformatics

Lecturer Prof. Dr. Daniel Huson
Lectures 

Mondays, Wednesdays 10-12h. (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.
Tutorials

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

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 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
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
22.11.21

continued

 
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  

15.12.21

10-12h

Exam part I -     in N 10, Hörsaalzentrum Morgenstelle

This covers chapters 1-7.

Assignment 08
20.12.21

8. Read mapping using the BWT or minimizers

 
22.12.21 continued Assignment 09
     
10.01.22 9. Minimap  
12.01.22

10. Genome assembly algorithms

Assignment 10
17.01.22 continued  
19.01.22 11.  RNA-seq Assignment 11
24.01.22 12. Population genetics  
26.01.22 13. Microbiome analysis Assignment 12
31.01.22 continued  
02.02.22 14. SVMs Practice exam
07.02.22 continued  
09.02.22

Exam part II - time and place not yet confirmed

This covers chapters 8-14.

 

 

   
Makeup exam

tbd

(There will be a makeup exam for both part I and for part II of the exam. These will take place back-to-back on the same day.)

 

 

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.