RNA Structure Prediction
• Rfam – RNA structures database• RNAfold – RNA secondary structure prediction• tRNAscan – tRNA prediction
Rfam
Different search modes
http://rfam.sanger.ac.uk/
Browse Rfam
:RibosomalRNA:Small RNA (mainly bacterial):Generally repressors of mRNA.:Catalytic RNA.:Small nuclear RNA (eukaryotes):Micro RNA,cytoplasmatic:Transfer RNA
:Parts of the mRNA involved in the regulation of it’s own activity:Internal ribosomal entry site
Search Rfam
Query
Subject
Structure
Hit
:::::: free extremes((())) Stem<<<>>> Internal Stem______ Loop,,,,,, Internal loop
Strucutre representaions
Link to EMBL
RNA structure prediction• Vienna RNA package:
• RNAfold predict minimum energy secondary
structures and pair probabilities
• RNAalifold predict consensus secondary structure• RNAeval evaluate energy of RNA secondary
structures
• RNAheat calculate the specific heat (melting
curve) of an RNA sequence
• RNAinverse inverse fold (design) sequences with
predefined structure
• RNAdistance compare secondary structures • RNApdist compare base pair probabilities • RNAsubopt complete suboptimal folding
RNA structure prediction
• Web interface available for RNAfold, RNAalifold, RNAinverse.
http://rna.tbi.univie.ac.at/cgi-bin/RNAfold.cgi
• Other can be downloaded for Unix and for Windows. http://www.tbi.univie.ac.at/~ivo/RNA/
RNA structure prediction
• RNAfold Gives best stabilized structure (structure with minimal free energy- mfe)
• RNAfold uses a dynamic programming algorithm that exploits base pairing and thermodynamic probabilities in order to predict the most likely structures of an RNA molecule (partition function algorithm).
Input sequence
Fold Algorithm: partition function recomended
RNA or DNA parameters
Target temperature
Advanced fold options
Output formats
Link to your previous run
Email (necessary for large sequences)
Sequence-Structure alignment
Free Energy
Enthalpy
Minimal free energy
Folding Probabiliy
Mountain Plot
• A mountain plot represents a secondary structure in a plot of height versus position.
• The height m(k) is given by the number of base pairs enclosing the base at position k.
• Loops correspond to plateaus and stems correspond to slopes.
• The closer the two curves, the better defined the structure.
Graphic representation
You can download SVG viewer from http://www.adobe.com/svg/viewer/install/
RNAfold structure representations
tRNAscana program for detection of transfer RNA genes in genomic sequencehttp://lowelab.ucsc.edu/tRNAscan-SE/
It can process very long sequences