Course lectured by Dr. Daniel Dörr from Bielefeld University, Germany, through the Erasmus teacher exchange program.
Genome rearrangements are mutations that permute blocks of DNA sequence in a genome. This class covers algorithmic techniques used in the computational analysis of genome rearrangement problems. The studied algorithms are mostly combinatorial by nature.
We start with the classical reversal distances which are measures to study chromosomal sequences only permuted by inversions. We then continue by discussing a general rearrangement distance and the double-cut-and-join (DCJ) distance. If time permits, we will discuss the problem of inferring genome rearrangements in the context of whole genome duplication events.
Required prior knowledge: basic knowledge of algorithms and data structures
Recommended prior knowledge: sequence analysis and foundations of genetics.
Aikataulu
Materiaalit
Inversion Visualization Software
Prof. Istvan Miklos, from the Bioinformatics Group (http://renyi.hu/staff/bioinf.html) in Alfréd Rényi Institute in Budapest, kindly shared his visualization software for the Breakpoint Graph. It is written in Java.
Usage: java InversionVisualisation file_name
For example: java InversionVisualisation example.txt
The input must be a signed permutation in one line, the numbers separated with a . There is an example in the provided archive.
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.
Muu
Kuvaus
After introductory bioinformatics courses and some algorithm courses have been taken.
8.1.-14.1.2018 MA 12-14, TI 10-14, KE 10-14, TO 10-14, PE 10-14.
(intensive period)
+ later agreed seminar day on period III.
Grading scale 1..5. Assessment is based on the exercise solutions and on the presentation.
Active attendance in lectures and exercise sessions. Students select a research article on the last lecture and prepare a presentation to be presented in a seminar organized during period III.