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

|[[http://ekvv.uni-bielefeld.de/kvv_publ/publ/vd?id=79062401|392109]]/[[http://ekvv.uni-bielefeld.de/kvv_publ/publ/vd?id=79062496|10]] | Stoye | Fr 8:45-10:15/Fr 10:15-11:45 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** |
| 21.10.2016 | Introduction, logistics | -- |
| 28.10.2016 | Physical mapping | {{:teaching:2016winter:alggr:exercises01Mapping.pdf|Exercises 1}} |
| 04.11.2016 | Genome assembly I,II,III | {{:teaching:2016winter:alggr:exercises02Assembly.pdf|Exercises 2}} |
| 11.11.2016 | Genome assembly IV | {{:teaching:2016winter:alggr:exercises03HybridAssembly.pdf|Exercises 3}} |
| 18.11.2016 | (no class) | -- |
| 25.11.2016 | (no class) | -- |
| 02.12.2016 | (no class) | -- |
| 09.12.2016 | Phylogenetic footprinting | {{:teaching:2016winter:alggr:exercises04Noncoding.pdf|Exercises 4}} |
| 16.12.2016 | RNA-seq | {{:teaching:2016winter:alggr:exercises05RNASeq.pdf|Exercises 5}} |
| 23.12.2016 | RNomics | {{:teaching:2016winter:alggr:exercises06RNAfolding.pdf|Exercises 6}} |
| 30.12.2016 | (no class) | -- |
| 06.01.2017 | (no class) | -- |
| 13.01.2017 | Proteomics: Analysis of mass spectra | {{:teaching:2016winter:alggr:exercises07MassSpec.pdf|Exercises 7}} |
| 20.01.2017 | Comparative genomics: detection of gene clusters | {{:teaching:2016winter:alggr:exercises08GeneClusters.pdf|Exercises 8}} |
| 27.01.2017 | (no class for health reasons)| |
| 03.02.2017 | Gene clusters part 2 (by Daniel Dörr) | slides: {{:teaching:2016winter:alggr:didiers_algorithm.pdf|Didier's Alg.}}, {{:teaching:2016winter:alggr:wci.pdf|weak CI}}|
| 10.02.2017 | Metagenomics (by Alexander Sczyrba) | -- |
==== Examination dates ====
Oral exams will be on 23.02.2017. Please make an appointment with the secretary in U10-151, Heike Samuel. 

If necessary, a second oral exam can be scheduled on an individual basis until end of March 2017. 

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