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
07.04.2014 Preliminaries / Sorting by Unsigned Reversals Slides Exercises
14.04.2014 Sorting by Unsigned Reversals II Slides Exercises
21.04.2014 (Holiday)
28.04.2014 Sorting by Signed Reversals I Slides Exercises
05.05.2014 Sorting by Signed Reversals II Slides Exercises
12.05.2014 Signed Reversals without hurdles and fortresses Slides Exercises
19.05.2014 Sorting by Translocations Slides Exercises
26.05.2014 The DCJ Operation Slides Exercises
02.06.2014 The DCJ-indel model and its potential to improve homology assignment Slides
09.06.2014 (Holiday)
16.06.2014 Multiple Genome Rearrangement and Breakpoint Models Slides Exercises
23.06.2014 Algebraic Theory for Genome Rearrangements Slides Exercises
30.06.2014 Applying Genome Rearrangements models in Real Data Slides Exercises
14.07.2014 Review and QA Review Exercises