====== Algorithms for Genome Rearrangement ======
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|392189/92 | Pedro Feijão | Mo 14:15-15:45/Mo 15:45-17:15 in U10-146 |[[http://ekvv.uni-bielefeld.de/kvv_publ/publ/vd?id=53686745|ekvv]]/[[http://ekvv.uni-bielefeld.de/kvv_publ/publ/vd?id=53686907|ekvv]] |

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



==== Software ====


=== Reversals and BP Graph ===
Prof. Istvan Miklos, from the [[http://renyi.hu/staff/bioinf.html|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 [[http://wiki.techfak.uni-bielefeld.de/gi/Teaching/2014summer/gr?action=AttachFile&do=get&target=Inversions.zip|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 | {{ 730lecture1_handout.pdf | Slides }} | {{ 730uebung01.pdf | Exercises }}|
| 20.04.2015 | Sorting by Unsigned Reversals II |  {{ 730lecture2-handout.pdf | Slides }} |  {{ 730uebung02.pdf | Exercises }}|
| 27.04.2015 | Sorting by Signed Reversals I | {{ 730lecture3.pdf | Slides }} | {{ 730uebung03.pdf | Exercises }}  |
| 04.05.2015 | Sorting by Signed Reversals II | {{ 730lecture4-handout.pdf | Slides }} |      {{ 730uebung04.pdf | Exercises }} |
| 11.05.2015 | Signed Reversals without hurdles and fortresses |  {{ 730Reversal-Mixtacki.pdf | Slides }} |  {{ 730uebung05.pdf | Exercises }} |
| 18.05.2015 | The DCJ Operation |  {{ 730lecture6.pdf | Slides }} | {{ 730uebung-06.pdf | Exercises }}|
| 01.06.2015 | Multiple Genome Rearrangement with the Breakpoint model | {{ 730lecture-mgr-bp-scj.pdf | Slides }} |  {{ 730uebung-mgr.pdf | Exercises }} |
| 08.06.2015 | The SCJ Operation |{{ 730lecture-scj.pdf | Slides }} |
| 15.06.2015 | The DCJ model with Insertions and Deletions |   {{ 730marilia-recombcg10.pdf | Slides }}   | {{ 730uebung-dcj-indel.pdf | Exercises }} |
| 29.06.2015 | The DCJ model with [[:InDels|InDels]] -- alternative model |   {{ 730Compeau - 2013 - DCJ-Indel sorting revisited.pdf | Paper }}   | {{ 730uebung-dcj-indel2.pdf | Exercises }} |
| 06.07.2015 | Tools for Real Data Analysis using Genome Rearrangements |    {{ 730lecture-practical.pdf | Slides }} | {{ 730uebung-yersinia.pdf | Exercises }} |
| 13.07.2015 | Algebraic Theory for Genome Rearrangements |    {{ 730lecture-algebraic.pdf | Slides }} |
| 20.07.2015 | Review exercises |    {{ 730uebung-review.pdf | Exercises }} |Back to [[:Teaching|Teaching]]