Algorithms in Genome Research

392109/10 Jens Stoye, Annelyse Thévenin, Pedro Feijão Fr 10:15-11:45/Fr 8:45-10:15 in U10-146 ekvv/ekvv


This class covers the basic algorithmic techniques used in the computational analysis of genome and post-genome data. This includes algorithms for genomic mapping and assembly, methods for functional genome annotation (gene finding and gene function prediction), algorithms for the analysis of DNA microarrays and mass spectra, methods and models for protein structure prediction, and algorithms for comparative genomics.


The page AlgGRLiterature contains many links to the original literature.


Reversals and BP Graph

Prof. Istvan Miklos, from the Bioinformatics Group in Alfréd Rényi Institute in Budapest, kindly shared his visualization software for the Breakpoint Graph. It is written in Java, and you can download it here.

Usage: java InversionVisualisation file_name

For example: java InversionVisualisation permutation.txt

The input must be a signed permutation in one line, the numbers separated with a TAB. There are some examples in the package.

Select the reality edges on which the reversal should act, and press the button Mutate. You can go forward and backward in the list of generated genomes, and you can delete any of them, too.

Time table:

Date Topic Exercises Name
11.10.2013 Introduction, logistics (none) all
18.10.2013 (no class) (none)
25.10.2013 Genome rearrangements - Reversals 1 Exercises Slides Pedro Feijão
01.11.2013 (no class)
08.11.2013 Genome rearrangements - Reversals 2 Exercises Slides Pedro Feijão
15.11.2013 Genome rearrangements - DCJ operation Exercises Slides Pedro Feijão
22.11.2013 Multiple Genome Rearrangements and Breakpoint Models Exercises Slides Pedro Feijão
29.11.2013 Assembly 1 Exercises Annelyse Thévenin
06.12.2013 Assembly 2 Exercises Annelyse Thévenin
13.12.2013 Genomic similarities 1 Exercises Annelyse Thévenin
20.12.2013 Genomic similarities 2 Exercises Slides1 Slides2 Annelyse Thévenin
10.01.2014 RNA sequencing Exercises Jens Stoye
17.01.2014 Computational Systems Biology Exercises Jens Stoye
24.01.2014 Haplotype inference Exercises Jens Stoye
31.01.2014 SNP-disease association mapping Exercises Jens Stoye
07.02.2014 Metagenomics, astrobiology Jens Stoye

Organisational Matters:

Together with the practical course “Bioinformatics Applications in Genome Research” in the following summer semester, this lecture forms the master module Algorithms in Genome Research.
The exercises will not be corrected or graded, but presence and activity during the exercise hours is expected. Credit points will be given based on an oral exam at the end of the semester.

Examination dates

Oral exam 11.02.2014 or 31.03.2014 Contact Heike Samuel for individual appointments