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

|[[http://ekvv.uni-bielefeld.de/kvv_publ/publ/vd?id=133280873|392109]]/[[http://ekvv.uni-bielefeld.de/kvv_publ/publ/vd?id=133281095|10]] | Braga, Stoye | Winter 2018/19 | 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** |
| 12.10.2018 | Introduction, logistics (M) | -- |
| 19.10.2018 | Physical mapping/consecutive ones problem (J) | {{:teaching:2018winter:alggr:exercises01PhysicalMapping.pdf|Exercises 1}} |
| 26.10.2018 | RNomics (J) | {{:teaching:2018winter:alggr:exercises02RNomics.pdf|Exercises 2}} |
| 02.11.2018 | Analysis of mass spectra (J) | {{:teaching:2018winter:alggr:exercises03MassSpec.pdf|Exercises 3}} |
| 09.11.2018 | -- | -- |
| 16.11.2018 | Genome assembly I (M) | {{:teaching:2018winter:alggr:exercises04OlcAssembly.pdf|Exercises 4}} |
| 23.11.2018 | Genome assembly II (M) | {{:teaching:2018winter:alggr:exercises05HtsAssembly.pdf|Exercises 5}}|
| 30.11.2018 | Genome assembly III (M) | {{:teaching:2018winter:alggr:exercises06AdvancedAssembly.pdf|Exercises 6}} and {{:teaching:2018winter:alggr:exercises06bAdvancedAssembly.pdf|6b}}|
| 07.12.2018 | Genome annotation I (J) | {{:teaching:2018winter:alggr:exercises07GeneFinding.pdf|Exercises 7}} |
| 14.12.2018 | Genome annotation II (J) | {{:teaching:2018winter:alggr:exercises08NonCoding.pdf|Exercises 8}} |
| 21.12.2018 | Haplotype inference, SNV-disease association mining (J) | {{:teaching:2018winter:alggr:exercises09HaplotypeInference.pdf|Exercises 9}} |
| X-mas break |||
| 11.01.2019 | Comparative genomics I (M) | {{:teaching:2018winter:alggr:exercises10Inversions.pdf|Exercises 10}} |
| 18.01.2019 | -- | -- |
| 25.01.2019 | Comparative genomics II (M) | {{:teaching:2018winter:alggr:exercises11Dcj.pdf|Exercises 11}} |
| 01.02.2019 | Comparative genomics III (M) | {{:teaching:2018winter:alggr:exercises12AncestralGenomes.pdf|Exercises 12}} |
| 08.02.2019 | Metagenomics (J) | -- |

==== Examination dates ====
Oral exams will be on 22.02.2019. Please make an appointment with the secretary in U10-151, Heike Samuel. 

A second oral exam can be taken on March 22, 2019. Please contact Heike Samuel if you are interested. 

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