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teaching:2019summer:bioappgere

Practical Course: Bioinformatics Applications in Genome Research


392181 Schulz Block 04.03.2019-15.03.2019 - 9:30-17:30 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” 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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teaching/2019summer/bioappgere.txt · Last modified: 2019/03/11 10:50 by Tizian Schulz