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