Algorithms for Sequence-based Bioinformatics

After having followed this course, the student has a good understanding of algorithms and data structures in genomics used for DNA sequence analysis. The student is able to implement algorithms in python, and can translate methods described in scientific literature into a working implementation.

Bioinformatics analyses in genomics aim to compare large sets of genomes in order to understand and explain differences in traits of an organism. Contemporary methods are powered by fundamental algorithms and data structures, which are efficient and scale to large data sets. A thorough understanding of these algorithms and data structures is necessary for advanced users and developers in this area.

Bioinformatics application domains that are covered include: variant calling, motif detection, genome assembly, sequence alignment, DNA sequencing.

The final grade of the course consists of the following components:

• Individual Assignments: programming exercises on foundational algorithms and data structures in bioinformatics sequence analysis (weighting 50%)

• Individual Report: reflection essay on group project product (weighting 10%)

• Group Assignment: group presentation on the benchmarking project including the student implementation and a literature derived implementation. Benchmarking project itself is assessed as a group assignment (weighting 40%)

Final grade calculation = 0.5 * Individual Assignments + 0.1 * Individual Report + 0.4 * Group Assignment

A passing final grade for the course can only be earned when for all components at least a 5.0 is earned, and the weighted final grade is at least a 5.8.

In case of an insufficient final result, repair options may exist in accordance with Article 17A, Times and number of examinations, sub 1, of the Teaching and Examination Regulations, for:

• Individual Assignments: Repair opportunity

• Individual Report: Repair opportunity

• Group Assignment: Repair opportunity

Disclaimer: information may change depending on unforeseen circumstances or measures (see: TER Art 2, sub 5).