Institute of Computer Science
University Freiburg

Practical Course: Applied Bioinformatics


Omer Alkhnbashi, A. Mitrofanov, S. Bray


1st meeting: 29.04.2019, 14:00

Course contents:

The course members will learn to use and understand biological sequence databases, perform searches, apply basic bioinformatic tools to answer common questions in bioinformatics. In addition, you will learn to solve basic bioinformatics questions using Python and visualise results with R. The course will be separated into blocks of six exercise sheets so that you will have to spend time on the course work equally throughout the semester. You should try to solve the exercises individually, but please contact us if you are stuck.


  1. DNA sequence databases & analysis, BLAST
  2. Protein sequence databases & analysis, multiple alignments, phylogenetic trees
  3. RNA sequence databases & analysis, folding, alignments, RNA-RNA interaction
  4. Real bioinformatics applications with Python

Requirements to pass the course:


Please hand in the exercise sheet in iPython Notebook format on time (hand-in date provided in brackets). 'Handwritten' hand-ins will not be accepted!
  • Introduction (29.04.2019) [pdf]
  • Exercise sheet 01 (until 12.05.2019, 23.59 hrs) [pdf] [fasta]
  • Protein sequence analysis (13.05.2019) [pdf]
  • Exercise sheet 02 (until 26.05.2019, 23.59 hrs) [pdf] [ex1 fasta] [ex5 fasta]
  • RNA structure analysis (27.05.2019) [pdf]