User Tools

Site Tools


teaching:2016summer:bioappgere

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 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
teaching/2016summer/bioappgere.txt · Last modified: 2016/11/03 09:18 by Pedro Feijao