====== Algorithms in Genome Research (Excerises) ======
\\ 


|392110 | Linda Sundermann, Alexander Sczyrba | Fr 8:30-12:00 in U10-146 | [[http://ekvv.uni-bielefeld.de/kvv_publ/publ/vd?id=33118688|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. \\ 

{{ 892genomescale.pdf | Script }} of the lessons hold by Veli Mkinen about genome scale algorithms. 



==== Time table (lecture): ====

| **Date** | **Topic** | **Exercises** |
| 19.10.2012 | Introduction, Logistics, Physical mapping | {{ 892exercises01mapping.pdf | Übungszettel 1 }} |
| 26.10.2012 | Assembly I | {{ 892exercises02assemblyI.pdf | Übungszettel 2 }} |
| 02.11.2012 | Assembly II | {{ 892exercises03assemblyII.pdf | Übungszettel 3 }} |
| 09.11.2012 | Dynamic Programming | {{ 892exercises04dynamicprogramming.pdf | Übungszettel 4 }} |
| 16.11.2012 | {{ 892bwtlecture.ppt | High troughput mapping with Borrows-Wheeler indexes }}| {{ 892exercises05hts_mapping_analysis.pdf | Übungszettel 5 }} |
| 23.11.2012 | BWT-based approaches, Transcipt expression detection| {{ 892exercises06BWT_chaining.pdf | Übungszettel 6 }} |
| 30.11.2012 | RNA sequencing, Overlap computation, {{ 892mums.pdf | MUMs }}| {{ 892exercises07advancedBW.pdf | Übungszettel 7 }} |
| 07.12.2012 | HMMs| {{ 892exercises08HMMs.pdf | Übungszettel 8 }} |
| 14.12.2012 | Gene finding| {{ 892exercises09hands-on_assembly.pdf | Übungszettel 9 }} |
| 21.12.2012 | Phylogenetic footprinting| {{ 892exercises10noncoding.pdf | Übungszettel 10 }} |
| 11.01.2013 | RNASeq| {{ 892exercises11RNASeq.pdf | Übungszettel 11 }} |

=== Further material ===
Phylogenetic Footprinting\\ {{ 892PhylFoot.pdf | Paper }} from Blanchette et al. 

Hands on Assembly\\ Nice website where you can cut out your reads and assemble them by hand: [[http://www.compbio.dundee.ac.uk/gigsaw/examples.html|http://www.compbio.dundee.ac.uk/gigsaw/examples.html]] 

PQ-Baum-Applet\\ Download {{ 892PQTree.jar | PQTree.jar }} and run java -jar PQTree.jar -g n where n is the number of leaves for the initial PQ-Tree. Select the elements which shall appear consecutively by mouse click and Ctrl or shift in the list on the left side of the window. Then click Reduce to get the resulting tree. Use Reset to get the initial tree again. //[Reference: J. Harris. A Graphical Java Implementation of PQ-Trees. www.jharris.ca/portfolio/academic.htm (last visited 09/20/2006), April 2002. Carleton University. Debugged by Roland Wittler, Bielefeld University.]// 

De Bruijn graphs\\ Paper by Compeau et al.: {{ 892deBruijn.pdf | How to apply de Bruijn grpahs to genome assembly }} 

SOLiD sequencing and mapping\\ {{ 892Voelkerding_2009.pdf | Next-generation sequencing: from basic research to diagnostics }}, Voelkerding et al., 2009 \\ {{ 892Rumble_2009.pdf | SHRiMP: Accurate Mapping of Short Color-space Reads }}, Rumble et al., 2009 \\ 



==== 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 | | ganztägig |
| Mündliche Prüfung |  | ganztägig |Back to [[:Teaching|Teaching]]