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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.

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slide1

RNA Structure Prediction

  • Rfam – RNA structures database
  • RNAfold – RNA secondary structure prediction
  • tRNAscan – tRNA prediction
slide2

Rfam

Different search modes

http://rfam.sanger.ac.uk/

slide3

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

slide5

Hit

Structure

Subject

Query

slide7

Strucutre representaions

:::::: free extremes

((())) Stem

<<<>>> Internal Stem

______ Loop

,,,,,, Internal loop

rna structure prediction
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 prediction1
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 prediction2
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).
slide13

Input sequence

RNA or DNA parameters

Fold Algorithm: partition function recomended

Target temperature

Advanced fold options

Output formats

Email (necessary for large sequences)

Link to your previous run

slide14

Sequence-Structure alignment

Free Energy

Enthalpy

slide15

Minimal free energy

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.

Folding Probabiliy

slide16

Graphic representation

You can download SVG viewer from http://www.adobe.com/svg/viewer/install/

slide18

tRNAscan

a program for detection of transfer RNA genes

in genomic sequence

http://lowelab.ucsc.edu/tRNAscan-SE/

It can process very long sequences