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


|392177 | Feijao | Summer semester 2016 | Block 07.03.2016-18.03.2016 - 9-17 Uhr in V6-116 |[[https://ekvv.uni-bielefeld.de/kvv_publ/publ/vd?id=70300573|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". 
  * Beside regular and active participation in the course, results shall also be presented to other participants. 


===== Overview =====

=== Day 1 - Shell ====
  * Exercises: Fabian

=== Day 2 - Assembly ===
  * Talk: Svenia: Genome Assembly, de Brujin Graphs
  * Exercises: Nikolaj

=== Day 3 - Finishing ===
  * Talk: BWA - Bianca
  * Exercises: Benedikt

=== Day 4 - Genome rearrangements ===
  * Talk: Rearrangement, DCJ - Cassandra
  * Exercises: Dimitri

=== Day 5 - Genome rearrangements II - DCJ ===
  * Talk: Circos tutorial - Pedro
  * Exercises: Bianca

=== Day 6 - Gene Prediction ===
  * Talk: Gene Prediction (software: Glimmer, Prodigal) - Fabian
  * Exercises: Cassandra

=== Day 7 - HMM ===
  * Talk: HMMs - Benedikt
  * Exercise: Svenia

=== Day 8 - Positional Scoring Matrices === 
  * Talk: PSSMs - Dimitri
  * Exercise: Nikolaj, Benedick, Bianca

=== Day 9 - Metagenomics === 
  * Talk: Metagenomics - Nikolaj
  * Exercise: Dimitri, Svenia, Cassandra

=== Day 10 - Finishing the Circos plot ===
  * Bringing cookies: Fabian