Algorithms for Genome Rearrangement

392189/92 Pedro Feijão Mo 14:15-15:45/Mo 15:45-17:15 in U10-146 ekvv/ekvv


This class covers algorithmic techniques used in the computational analysis of genome rearrangement problems.


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
13.04.2015 Preliminaries / Sorting by Unsigned Reversals I Slides Exercises
20.04.2015 Sorting by Unsigned Reversals II Slides Exercises
27.04.2015 Sorting by Signed Reversals I Slides Exercises
04.05.2015 Sorting by Signed Reversals II Slides Exercises
11.05.2015 Signed Reversals without hurdles and fortresses Slides Exercises
18.05.2015 The DCJ Operation Slides Exercises
01.06.2015 Multiple Genome Rearrangement with the Breakpoint model Slides Exercises
08.06.2015 The SCJ Operation Slides
15.06.2015 The DCJ model with Insertions and Deletions Slides Exercises
29.06.2015 The DCJ model with InDels – alternative model Paper Exercises
06.07.2015 Tools for Real Data Analysis using Genome Rearrangements Slides Exercises
13.07.2015 Algebraic Theory for Genome Rearrangements Slides
20.07.2015 Review exercises Exercises