RNA Structure Prediction Rfam – RNA structures database RNAfold – RNA secondary structure prediction tRNAscan – tRNA prediction.

RNA Structure Prediction

• Rfam – RNA structures database• RNAfold – RNA secondary structure prediction• tRNAscan – tRNA prediction

Rfam

Different search modes

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