Practical Course: Bioinformatic Applications in Genome Research

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.

• Exercises: Fabian

• Talk: Svenia: Genome Assembly, de Brujin Graphs
• Exercises: Nikolaj

• Talk: BWA - Bianca
• Exercises: Benedikt

• Talk: Rearrangement, DCJ - Cassandra
• Exercises: Dimitri

• Talk: Circos tutorial - Pedro
• Exercises: Bianca

• Talk: Gene Prediction (software: Glimmer, Prodigal) - Fabian
• Exercises: Cassandra

• Talk: HMMs - Benedikt
• Exercise: Svenia

• Talk: PSSMs - Dimitri
• Exercise: Nikolaj, Benedick, Bianca

• Talk: Metagenomics - Nikolaj
• Exercise: Dimitri, Svenia, Cassandra

• Bringing cookies: Fabian