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teaching:2018summer:bioappgere

Practical Course: Bioinformatics Applications in Genome Research


392181 Schulz Block 12.03.2017-23.03.2017 - 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, 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

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teaching/2018summer/bioappgere.txt · Last modified: 2018/03/12 16:36 by Tizian Schulz