====== Algorithms in Genome Research ======

|[[https://ekvv.uni-bielefeld.de/kvv_publ/publ/vd?id=176725328|392109]]/[[https://ekvv.uni-bielefeld.de/kvv_publ/publ/vd?id=176725812|10]] | Braga, Dörr | Winter 2019/20 | Fr 9:00-10:30 and 10:30-12:00 in U10-146 |

==== Contents ====
This class covers the basic algorithmic techniques used in the computational analysis of genome and post-genome data. This includes algorithms for genomic mapping and assembly, methods for functional genome annotation (gene finding and gene function prediction), algorithms for the analysis of DNA microarrays and mass spectra, methods and models for protein structure prediction, and algorithms for comparative genomics. 

==== Literature ====
The page [[teaching:alggrliterature|AlgGRLiterature]] contains many links to the original literature. 

==== Time table ====

| **Date** | **Topic** | **Exercises/Addenda** |
| 11.10.2019 | Introduction, logistics (M)  | -- |
| 18.10.2019 | Genome Assembly 1 (M) | {{:teaching:2019winter:alggr:exercises01OlcAssembly.pdf|Exercises 1}} |
| 25.10.2019 | Genome Assembly 2 (M) | {{:teaching:2019winter:alggr:exercises02HtsAssembly.pdf|Exercises 2}} |
| 01.11.2019 | (Allerheiligen) ||
| 08.11.2019 | Genome Assembly 3 (M) | {{:teaching:2019winter:alggr:exercises03AdvancedAssembly.pdf|Exercises 3}} |
| 15.11.2019 | Physical Mapping (D)  | {{:teaching:2019winter:alggr:exercises04physicalmapping.pdf|Exercises 4}}|
| 22.11.2019 | Hi-C Data Analysis 1 (D) | -- |
| 29.11.2019 | Hi-C Data Analysis 2 (D) | {{:teaching:2019winter:alggr:exercises05hicdataanalysis.pdf|Exercises 5}} |
| 06.12.2019 | Conservation Ecology (D) | {{:teaching:2019winter:alggr:TSP_LPs.tar.bz2|Linear Programs}} |
| 09.12.2019 | Perfect Phylogeny and Cancer (D) | {{:teaching:2019winter:alggr:exercises06perfectphylogeny.pdf|Exercises 6}}, {{:teaching:2019winter:alggr:ILPs.tar.bz2|Integer Linear Programs}}  |
| 20.12.2019 | Metagenomics (R) | {{:teaching:2019winter:alggr:exercises07metagenomics.pdf|Exercises 7}} |
| (X-mas break) |||
| 10.01.2020 | Haplotype Inference (D) | {{:teaching:2019winter:alggr:exercieses08haplotypeinference.pdf|Exercises 8}} |
| 17.01.2020 | Double-Cut-And-Join (D) | {{:teaching:2019winter:alggr:exercises09dcj.pdf|Exercises 9}}, {{:teaching:2019winter:alggr:skript_04.pdf|Lecture Notes}}|
| 24.01.2020 | Inversions (M) | {{:teaching:2019winter:alggr:exercises10binversions.pdf|Exercises 10b}} |
| 31.01.2020 | SCJ (M) | -- |

==== Examination dates ====

February 27, 2020

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