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


|392109/10 | Jens Stoye | Fr 10:15-11:45/Fr 8:45-10:15 in U10-146 |[[http://ekvv.uni-bielefeld.de/kvv_publ/publ/vd?id=25663292|ekvv]]/[[http://ekvv.uni-bielefeld.de/kvv_publ/publ/vd?id=25663869|ekvv]] |

==== 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** |
| 14.10.2011 | Introduction, logistics | (none) |
| 21.10.2011 | (no class) | --- |
| 28.10.2011 | (no class) | --- |
| 04.11.2011 | De-novo HTS genome assembly | {{ 957exercises01HtsAssembly.pdf | Number 1 }}|
| 11.11.2011 | Comparative HTS genome assembly | {{ 957exercises02ComparativeAssembly.pdf | Number 2 }}|
| 18.11.2011 | RNA and protein-coding gene finding | {{ 957exercises03GeneFinding.pdf | Number 3 }}|
| 25.11.2011 | Finding patterns in non-coding regions | {{ 957exercises04Noncoding.pdf | Number 4 }}|
| 02.12.2011 | RNA-seq | {{ 957exercises05RNASeq.pdf | Number 5 }}|
| 09.12.2011 | Analysis of mass spectra ({{ 957MassSpecExample.pdf | Example }})| {{ 957exercises06MassSpec.pdf | Number 6 }}|
| 16.12.2011 | Genome rearrangement | {{ 957exercises07Dcj.pdf | Number 7 }}|
| 23.12.2011 | Genome halving | {{ 957exercises08GenomeHalving.pdf | Number 8 }}|
| 30.12.2011 | --- christmas break --- | --- |
| 06.01.2012 | --- christmas break --- | --- |
| 13.01.2012 | Gene clusters | {{ 957exercises09GeneClusters.pdf | Number 9 }}|
| 20.01.2012 | Reconstruction of ancestral genomes (by Roland Wittler)| {{ 957exercises10AncestralGenomes.pdf | Number 10 }} \\{{ 957coryne.tree | phylogenetic tree }} \\ {{ 957coryne.csd | gene order data }}|
| 27.01.2012 | Haplotype inference and SNP-disease association mining | {{ 957exercises11AssociationMapping.pdf | Number 11 }}|
| 03.02.2012 | Metagenomics and astrobiology | --- |

==== Organisational Matters: ====
Together with the practical course "Bioinformatics Applications in Genome Research" in the following summer semester, this lecture forms the master module [[http://www.zfl.uni-bielefeld.de/studium/module/techfak/modulhandbuch/#algorithmen_genomforschung|Algorithms in Genome Research]].\\ The exercises will not be corrected or graded, but presence and activity during the exercise hours is expected. Credit points will be given based on an oral exam at the end of the semester. 



==== Prüfungstermine ====

| Mündliche Prüfung | Mo 27.02.2012 | ganztägig |
| Mündliche Prüfung | Di 28.02.2012 | ganztägig |Back to [[:Teaching|Teaching]]