Next:
RNA Web Services
A short Tutorial on RNA Bioinformatics
The ViennaRNA Package and related Programs
RNA Web Services
Useful Web Services
Prerequisites to get started
Typographical Conventions
Data Files
Terminal, Command line and Editor
Terminal and Command
Core Unix Commands
Installing Software from Source
Get the
ViennaRNA Package
Build the
ViennaRNA Package
Build the
ViennaRNA Package
What's in the
ViennaRNA Package
The base directory
Which programs are available?
Which Utilities are available?
The Input File Format
Structure Prediction on single Sequences
The Program
RNAfold
MFE structure of a single sequence
Predicting equilibrium pair probabilities
Secondary Structure plot and Dot plot
Mountain and Reliability plot
The Program
RNAsubopt
Suboptimal folding
Sampling the Boltzmann Ensemble
RNA folding kinetics
RNA2Dfold
barriers & treekin
A short recall on howto install/compile a program
Calculate the Barrier Tree
Calculate The Barrier Tree
Simulating the Folding Kinetics
Sequence Design
The Program
RNAinverse
Sequence Design
switch.pl
Designing a Switch
RNA-RNA Interactions
The Program
RNAcofold
Two Sequences one Structure
Secondary Structure Plot and Dot Plot
Concentration Dependency
Concentration Dependency
Concentration Dependency plot
Finding potential binding sites with
RNAduplex
Binding site prediction with
RNAduplex
Consensus Structure Prediction
The Program
RNAalifold
Consensus Structure from related Sequences
RNAalifold
Output Files
Structure predictions for the individual sequences
Refolding Individual Sequences
Refolded structure of E. coli RNase P
Structural Alignments
Manually correcting Alignments
Automatic structural alignments
Install r-Coffee
About this document ...
Sven Findeiss 2013-11-22