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

|[[https://ekvv.uni-bielefeld.de/kvv_publ/publ/vd?id=288194423|392109]]/[[https://ekvv.uni-bielefeld.de/kvv_publ/publ/vd?id=288195757|10]] | Stoye | Winter 2021/22 | 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** |
| 15.10.2021 | no class | -- |
| 22.10.2021 | Introduction, logistics | -- |
| 29.10.2021 | no class | -- |
| 05.11.2021 | Physical mapping/consecutive ones problem | {{:teaching:2021winter:alggr:exercises01PhysicalMapping.pdf|Exercises 1}} |
| 12.11.2021 | Genome assembly I | {{:teaching:2021winter:alggr:exercises02Assembly1.pdf|Exercises 2}} |
| 19.11.2021 | Genome assembly II | {{:teaching:2021winter:alggr:exercises03Assembly2.pdf|Exercises 3}} |
| 26.11.2021 | Genome annotation | {{:teaching:2021winter:alggr:exercises04GenomeAnnotation.pdf|Exercises 4}} |
| 03.12.2021 | no class | -- |
| 10.12.2021 | Sequence alignment | {{:teaching:2021winter:alggr:exercises05Alignment.pdf|Exercises 5}} |
| 17.12.2021 | Transcriptomics (RNA sequencing) | {{:teaching:2021winter:alggr:exercises06RNASeq.pdf|Exercises 6}} |
| X-mas break |||
| 07.01.2022 (XXL) | RNA secondary structure prediction, analysis of mass spectra | {{:teaching:2021winter:alggr:exercises0708RNAFoldingMassSpec.pdf|Exercises 7/8}} |
| 14.01.2022 | Haplotype inference | {{:teaching:2021winter:alggr:exercises09Haplotypes.pdf|Exercises 9}} |
| 21.01.2022 | SNP-disease association mapping | {{:teaching:2021winter:alggr:exercises10AssociationMapping.pdf|Exercises 10}} |
| 28.01.2022 | Computational pangenomics | {{:teaching:2021winter:alggr:exercises11Pangenomics.pdf|Exercises 11}} |
| 04.02.2022 | Computational metagenomics | -- |
| 25.02.2022 | Computational metagenomics - again | -- |

==== Examination dates ====
Oral exams (in presence) will be on 18 February 2022 or later. 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 2022. Please contact Heike Samuel if you are interested.