Algorithms in Bioinformatics

BIOINF2110AB Proseminar Foundations of Bioinformatics

Teachers Prof Daniel Huson and Timo Lucas
Date Tuesdays, 8:15-10 a.m.
Starts 26th October 8:15-10:00 a.m.
Register via Ilias
Language English
Links Alma Ilias


The aim of this proseminar is to obtain an overview and introduction to some of the fundamental topics in bioinformatics. 

In the first session of the proseminar, we will provide an overview over the topics to be discussed in the seminar and then the topics will be assigned to the participants. Each participant will be provided with one or more papers on their topic. In addition, participants are expected to also survey the literature so as to identify additional papers that are useful for their topic.

Each participant will give a 20-25 minute oral presentation, followed by questions and discussion, and then feedback. Sessions will be chaired by a participant of the seminar. In addition, each participant will provide a write-up of their topic (~12 pages) in which they present the content of their presentation in their own words. 

Grading will be based on the quality of the oral presentation. The quality of the writeup and the level of participation in discussions will used to adjust the grade (up or down). Participation in all sessions is mandatory.

To ensure a high quality of presentations and write-ups, each participant must discuss their presentation with their supervisor at least one week before the scheduled presentation. The write-up is due two weeks after the presentation, at the latest.


Date Topic Student Supervisor
26th October Overview and topic selection    
30th Nov.

Community profiling using QIIME

30th Nov.

Metagenome analysis using MEGAN

7th Dec.

Taxonomic metagenome analysis using MetaPhlAn

7th Dec.

Functional metagenome analysis using HUMAnN2

14th Dec.

Microbiome analysis using Kraken

14th Dec.

Metagenome asssembly using MegaHit

21st Dec.

MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies

21st Dec.

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

11th Jan. 2022

Minimap2: pairwise alignment for nucleotide sequences

11th Jan. 2022

Mash: fast genome and metagenome distance estimation using MinHash

18th Jan. 2022

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

18th Jan. 2022

Prokka: rapid prokaryotic genome annotation


Additional possible topics:



  • Topics are handed out in class.
  • Students are first required to determine literature and other sources that are suitable to address their topic. The result of the literature search should be discussed with the tutor before students starts working on their report and presentation.
  • The first page of the report and the first slide should contain the title of the seminar and the presentation, the student's name and email address and the tutor's name and the date.
  • If figures, formulations or whole sentences are taken verbally from the references it has to be marked as a citation; this is also the case if the reference is a WWW document, there the exact url and the author of the text have to be cited.
  • Presentation and report in English.


  • The quality of the presentation and the report will be assessed on content and presentation and a total grade will be given by the tutors.