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

|[[https://ekvv.uni-bielefeld.de/kvv_publ/publ/vd?id=228329132|392109]]/[[https://ekvv.uni-bielefeld.de/kvv_publ/publ/vd?id=228331454|10]] | Stoye | Winter 2020/21 | Fr 9:00-10:30 and 10:30-12:00 in X-E1-200 |
==== 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** | **Notes** |
| 30.10.2020 | Introduction, logistics | -- | -- |
| 06.11.2020 | Physical mapping | {{:teaching:2020winter:alggr:exercises01PhysicalMapping.pdf|Exercises 1}} | -- |
| 13.11.2020 | Genome assembly I | {{:teaching:2020winter:alggr:exercises02Assembly1.pdf|Exercises 2}} | -- |
| 20.11.2020 | Genome assembly II | {{:teaching:2020winter:alggr:exercises03Assembly2.pdf|Exercises 3}} | -- |
| 27.11.2020 | Genome annotation I | {{:teaching:2020winter:alggr:exercises04GeneFinding.pdf|Exercises 4}} | -- |
| 04.12.2020 | Genome annotation II | {{:teaching:2020winter:alggr:exercises05Noncoding.pdf|Exercises 5}} | {{:teaching:2020winter:alggr:notes05Noncoding.pdf|Notes 5}} |
| 11.12.2020 | RNA sequencing | {{:teaching:2020winter:alggr:exercises06RNASeq.pdf|Exercises 6}} | {{:teaching:2020winter:alggr:notes06RNASeq.pdf|Notes 6}} |
| 18.12.2020 | Analysis of mass spectra | {{:teaching:2020winter:alggr:exercises07MassSpec.pdf|Exercises 7}} | {{:teaching:2020winter:alggr:notes07MassSpec.pdf|Notes 7}} |
| X-mas break ||||
| 08.01.2021 | SNV-disease association mapping | {{:teaching:2020winter:alggr:exercises08AssociationMapping.pdf|Exercises 8}} | {{:teaching:2020winter:alggr:notes08AssociationMapping.pdf|Notes 8}} |
| 15.01.2021 | Pangenomics | {{:teaching:2020winter:alggr:exercises09Pangenomics.pdf|Exercises 9}} | {{:teaching:2020winter:alggr:notes09Pangenomics.pdf|Notes 9}} |
| 22.01.2021 | Haplotype inference | {{:teaching:2020winter:alggr:exercises10HaplotypeInference.pdf|Exercises 10}} | {{:teaching:2020winter:alggr:notes10HaplotypeInference.pdf|Notes 10}} |
| 29.01.2021 | Comparative genomics I: Genome rearrangement | {{:teaching:2020winter:alggr:exercises11GenomeRearrangement.pdf|Exercises 11}} | {{:teaching:2020winter:alggr:notes11GenomeRearrangement.pdf|Notes 11}} |
| 05.02.2021 | Comparative genomics II: Gene cluster detection |  {{:teaching:2020winter:alggr:exercises12GeneClusters.pdf|Exercises 12}} | {{:teaching:2020winter:alggr:notes12GeneClusters.pdf|Notes 12}} |
| 12.02.2021 | Metagenomics | -- | {{:teaching:2020winter:alggr:notes13Metagenomics.pdf|Notes 13}} |

==== Examination dates ====
Oral exams will be on 19 February 2021, either presential (if permitted) or online via Zoom. Please make an appointment with the secretary in U10-151, [[https://ekvv.uni-bielefeld.de/pers_publ/publ/PersonDetail.jsp?personId=65856&lang=EN|Heike Samuel]].

A second oral exam can be taken in March 2021. Please contact Heike Samuel if you are interested.