====== Practical Course: Bioinformatics Applications in Genome Research ======
\\ 


| 392181  | Schulz  | Block 12.03.2017-23.03.2017 - 9:30-17:30 Uhr in V6-116  | [[https://ekvv.uni-bielefeld.de/kvv_publ/publ/vd?id=119694679|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, 12.3. | Shell                   | Tizian: //Introduction to Python// | Christina |
| Tue, 13.3. | Assembly                | Jan: //Genome Assembly, de Brujin Graphs// | Christina |
| Wed, 14.3. | Finishing               | Jan: //BWA// | Maria |
| Thu, 15.3. | Genome rearrangements I | Maria: //Rearrangement distances// | Jan |
| Fri, 16.3. | Genome rearrangements II| Maria: //Circos tutorial// | Yannik |
| Mon, 19.3. | Gene Prediction         | Yannik: //Gene Prediction (software: Glimmer, Prodigal)// | Jan |
| Tue, 20.3. | Hidden Markov Models (HMMs)| Yannik: //HMMs// | Yannik |
| Wed, 21.3. | Position-Specific Scoring Matrices (PSSMs)| Christina: //PSSMs// | Maria |
| Thu, 22.3. | Metagenomics            | Christina: //Metagenomics// | -- |
| Fri, 23.3. | Finishing the Circos plot  | -- | -- |


----
Back to [[:teaching|Teaching]]