RNA Strukturvorhersage und -vergleich (WS 20xx)

RNA Structure Prediction and Comparison (WS 2012/2013) ::

Course home page

This page shows the course slides, as used in the WS 2011 version of the lecture, and provides articles for further reading. Initially, most slide files are versions from the winter 2011 lecture, which will be updated as the 2012 course proceeds.

Final examination

The final exam has been scheduled to Thursday, Feb. 7 and Friday, Feb. 8. As these will be individual, oral examinations, see our secretary for individual date and hour.

There will be an "open question sesssion" to prepare for the exam, in the last course session on Jan. 28.

Required readings for the examination:

Lecture Materials:

Part 1: Single sequence structure prediction

Session 1: RNA-Biology Background
Session 2: Structure Representations
Session 3: RNA folding
Session4: Abstract Shape Analysis
Session 5a: Effects of variants in the energy model implementation
Session 5b: Folding RNA with pseudoknots, including kissing hairpin structures

Note; This semester, Part 4 of this lecture was held right after part 2.

Part 2: Comparative structure prediction

Session 6a:Comparative Structure Prediction -- Part 1
Session 6b:Comparative Structure Prediction -- Part 2
Session 7:Plan A: RNAalifold, Plan B: Locarna
Session 8:Plan C: RNAforecast based on consensus shapes Covered within Session 4.

Part 3: Stochastic models

Session 9: Stochastic context free grammars for structure prediction This is an introductory textbook chapter on the topic of this and the next session.
Session 10: Stochastic RNA family models. Additional background reading: RNA family models; additional slides in Infernal RNA homology search

Part 4: Structure comparison

Session 11: Models of Structure Comparison
Additional Reading: A very nice chapter from Matthias Höchsmann's thesis
Session 12: The Tree Alignment Algorithm (with affine gaps and anchors)
additional reading: Details of Tree Alignment, Multiple Tree Alignment and RNAforester

Part 5: Selected special topics

Note: These are some topics from earlier issues of this lecture, not covered in 2011

Session 13: Folding RNA Pseudoknots (Part 1)and Folding RNA Pseudoknots (Part 2).
See also the recent article on kissing hairpin prediction.
Session 14: Short talks and open problem session
Session 15: RNA Gene prediction
Session 16: MicroRNA Target Prediction with RNAhybrid
Session 17: The RNA world hypothesis[14]

Literature:

AbstractShapes.pdf (Session 4)
ConsensusShapes.pdf (Session 10)
Background reading from Theory in Biosciences (Review on known families of functional RNAs)
RibosomeStructure.pdf (Review from SCIENCE 2005 on RNA tertiary structure)
RNAz

$Author: robert $$Date: 2011/10/10 $