Bachelor and master thesis projects

Bachelor and Master theses

Our research projects provide permanently new topics for bachelor and master theses. We are happy to adapt the topic of a thesis work to your experience and interests.

Particularly, we currently propose one project for a bachelor and master thesis:

Wavefront transformation and alignment of protein sequences

Protein sequence alignment is a fundamental and widely-used technique in bioinformatics. Its computational costs often require heuristic approaches for database searches, such as BLAST and others. Our SIMAP 2 project, however, maintains a sequence similarity matrix that is calculated with the exact Smith-Waterman algorithm. SIMAP 2 thus provides maximum sensitivity of pairwise alignments and is the basis for large-scale inference of orthologous groups, e.g. in EGGNOG and STRING. Recently, a new algorithm has been published that accelerates Smith-Waterman alignment calculation using a wavefront transformation. The task of this bachelor or master project is to evaluate the correctness and performance of this new acceleration idea. The thesis requires substantial programming skills. Basic knowledge in machine learning and GPU programming are helpful. The results of this thesis will directly contribute to the further improvement of our SIMAP 2 project.

If you are interested and have a good background in bioinformatics, we are very happy to present you these topics in detail during a personal meeting. Please contact Thomas Rattei for more information.