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--- teaching:2018summer:cg [2018/09/11 15:41]
+++ teaching:2018summer:cg [2020/02/14 09:07] (current)
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+====== 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.
+----
+Back to [[:teaching|Teaching]]

Genome Informatics

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