====== Practical Course: Bioinformatics Applications in Genome Research ======
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| 392181  | Schulz  | Block 04.03.2019-15.03.2019 - 9:30-17:30 Uhr in V6-116  | [[https://ekvv.uni-bielefeld.de/kvv_publ/publ/vd?id=152987362|ekvv]]  |

===== Content =====
In this course, practical applications and issues in concrete problem statements and handling real data sets will be addressed. The following topics are intended: assembly, scaffolding, annotation, gene prediction, comparative analysis, etc.  

Theoretical knowledge of the students shall be supplemented by practical aspects such as setting up and running existing tools, implementing small own tools, pre- and postprocessing, and critical interpretation of results. A continuously enriched visualization of the data and the obtained results will also guide through the course. 


  * Requires participation in the lecture "Algorithms in Genome Research" or similar. 
  * Beside regular and active participation in the course, each student gives a short (15min) presentation and presents their results to the other participants. 

===== Overview =====

| **Date**    | **Topic**                                   | **Presentation**                                           | **Solution (for next day)**  |
| Mon, 4.3.   | Shell                                       | Tizian: //Introduction to Python//                         | Timo                         |
| Tue, 5.3.   | Assembly                                    | Andreas: //Genome Assembly, de Brujin Graphs//             | Andreas                      |
| Wed, 6.3.   | Finishing                                   | Andreas: //BWA//                                           | Andreas                      |
| Thu, 7.3.   | Genome rearrangements I                     | Timo: //Rearrangement distances//                          | Timo                         |
| Fri, 8.3.   | Genome rearrangements II                    | Kevin: //Circos tutorial//                                 | Kevin                        |
| Mon, 11.3.  | Gene Prediction                             | Giulia: //Gene Prediction (software: Glimmer, Prodigal)//  | Giulia                       |
| Tue, 12.3.  | Hidden Markov Models (HMMs)                 | Giulia: //HMMs//                                           | Giulia                       |
| Wed, 13.3.  | Position-Specific Scoring Matrices (PSSMs)  | Kevin: //PSSMs//                                           | Kevin                        |
| Thu, 14.3.  | Metagenomics                                | Timo: //Metagenomics//                                     | Everyone                     |
| Fri, 15.3.  | Finishing the Circos plot                   | --                                                         | --                           |


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