Implementation of Algorithms (1Ü)

392041 Stoye Winter 2022/23 Class hours by appointment


Each participant implements a (simple) algorithm in a programming language of their own choice. Topics will be distributed individually: meet or send email to the organizer, or to a lecturer of any other class in the modules Algorithms in Bioinformatics or Special Algorithmus in Bioinformatics. The focus of the implementation shall be on code readability and optimal asymptotics, which ideally is verified by systematic testing.

The source code and some test data (where applicable) has to be sent to the organizer one week before the final presentation. During the final presentation, every participant runs and explains her/his software in front of everybody. If the result is not satisfactory, a correction can be provided until the end of the semester.

Final presentation:

Monday, 2023 January 30, at 14h c.t., U10-146.

Distributed topics:

Topic Name
Global sequence alignment with affine gap costs (Gotoh Algorithm) Presian A
Minimum mutation problem, general version (Fitch/Sankoff Algorithm) Franziska H
Neighbor Joining Nikolas V
BWT construction and search Lisa Marie H
Agglomerative clustering, various methods Leonie B
Counting k-mers Jamie S