====== Algorithms in Comparative Genomics (2V + 2Ü) ======

| 392189/92 | Stoye | Summer 2018 | Fr 08:45 - 10:15 (Ü), Fr 10:15 - 11:45 (V) in U10-146 | [[https://ekvv.uni-bielefeld.de/kvv_publ/publ/vd?id=118943515|ekvv]]/[[https://ekvv.uni-bielefeld.de/kvv_publ/publ/vd?id=118943979|ekvv]] |

===== Content =====

Many questions in molecular biology, phylogenetics, and biomedicine can be approached through comparison of two or more genomes. However, a global alignment of multiple large genomes is often infeasible or comes at great expense. It is more efficient to compare genomes on a higher level of abstraction, as given by the succession of single-copy genes or other kinds of unique genomic markers on the chromosomal sequences. 

In this course, various models of higher level genome comparison are discussed. We start with the classical breakpoint distance, followed by other simple measures such as SC/J and DCJ. The reversal distance will be discussed, and a general genome rearrangement distance, the so-called Hannenhalli-Pevzner distance. It then follows a discussion of methods that solve the problem of comparing sequences with unequal gene/marker content. We will also study methods for the reconstruction of ancestral genomes.

Algorithms discussed in this course are mostly combinatorial by nature, similar to the sequence analysis course.

This course is taught in English.
===== Conditions for participation, prior knowledge =====

Required: Algorithms and Data Structures (or comparable)\\
Recommended: Sequence Analysis and Foundations of Genome Research

===== Schedule =====

| **Date**    | **Topic**                                 | **Exercises**  | ** Literature ** |
| 13.04.2018  | Organizational matters (just 10 minutes)  | --             | -- |
| 20.04.2018  | -- no class --                            | --             | -- |
| 27.04.2018  | Introduction                              | --             | -- |
| 04.05.2018  | Breakpoint Distance | {{:teaching:2018summer:cg:exercises01BpDistance.pdf|Exercises 1}} | [[https://doi.org/10.1186/1471-2105-10-120|Tannier et al. 2009]] |
| 11.05.2018  | Single Cut or Join Distance and Sorting | {{:teaching:2018summer:cg:exercises02Scj.pdf|Exercises 2}} | [[https://doi.org/10.1109/TCBB.2011.34|Feijão & Meidanis 2011]] |
| 18.05.2018  | -- no class --                            | --             | -- |
| 25.05.2018  | Double Cut and Join Distance and Sorting  | {{:teaching:2018summer:cg:exercises03Dcj.pdf|Exercises 3}} | [[https://doi.org/10.1007/11851561_16|Bergeron et al. 2006]] |
| 01.06.2018  | Reversal Distance and Sorting             | {{:teaching:2018summer:cg:exercises04Reversals.pdf|Exercises 4}} | [[https://link.springer.com/chapter/10.1007/978-3-540-27801-6_29|Bergeron et al. 2004]] |
| 08.06.2018  | The Genomic Distance and Sorting          | {{:teaching:2018summer:cg:exercises05Hp.pdf|Exercises 5}} | [[https://doi.org/10.1016/j.tcs.2009.09.008|Bergeron et al. 2009]],\\ [[https://doi.org/10.1016/j.aml.2010.08.021|Erdős et al. 2011]] |
| 15.06.2018  | Double Cut and Join with Indels           | {{:teaching:2018summer:cg:exercises06DcjIndel.pdf|Exercises 6}} | [[https://doi.org/10.1089/cmb.2011.0118|Braga et al. 2011]] |
| 22.06.2018  | Multiple Genomes                          | {{:teaching:2018summer:cg:exercises07MultipleGenomes.pdf|Exercises 7}}\\ ({{:teaching:2018summer:cg:coryne_tree.txt|phylogenetic tree}},\\ {{:teaching:2018summer:cg:coryne_csd.txt|gene order data}}) | [[https://doi.org/10.1186/1471-2105-16-S14-S3|Feijão 2015]] |
| 29.06.2018  | Genome Halving                            | {{:teaching;2018summer:cg:exercises08genomehalving.pdf|Exercises 8}} | [[https://doi.org/10.1007/978-3-540-69733-6_28|Mixtacki 2008]] |
| 06.07.2018  | Family-free Genome Comparison             | {{:|Exercises 9}} | [[https://doi.org/10.1007/978-1-4471-5298-9_13|Braga et al. 2013]], [[https://doi.org/10.1007/978-1-4939-7463-4_12|Doerr et al. 2018]] |
| 13.07.2018  | -- no class --                            | --             | -- |
| 20.07.2018  | Oral exams                                | --             | -- |

Further oral exams can be scheduled on an individual basis.

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