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

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Page 1: 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

Page 2: RNA Structure Prediction Rfam – RNA structures database RNAfold – RNA secondary structure prediction tRNAscan – tRNA prediction

Rfam

Different search modes

Page 3: RNA Structure Prediction Rfam – RNA structures database RNAfold – RNA secondary structure prediction tRNAscan – tRNA prediction

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

Page 4: RNA Structure Prediction Rfam – RNA structures database RNAfold – RNA secondary structure prediction tRNAscan – tRNA prediction

Search Rfam

Page 5: RNA Structure Prediction Rfam – RNA structures database RNAfold – RNA secondary structure prediction tRNAscan – tRNA prediction

Query

Subject

Structure

Hit

Page 6: RNA Structure Prediction Rfam – RNA structures database RNAfold – RNA secondary structure prediction tRNAscan – tRNA prediction
Page 7: RNA Structure Prediction Rfam – RNA structures database RNAfold – RNA secondary structure prediction tRNAscan – tRNA prediction

:::::: free extremes((())) Stem<<<>>> Internal Stem______ Loop,,,,,, Internal loop

Strucutre representaions

Page 8: RNA Structure Prediction Rfam – RNA structures database RNAfold – RNA secondary structure prediction tRNAscan – tRNA prediction
Page 9: RNA Structure Prediction Rfam – RNA structures database RNAfold – RNA secondary structure prediction tRNAscan – tRNA prediction

Link to EMBL

Page 10: RNA Structure Prediction Rfam – RNA structures database RNAfold – RNA secondary structure prediction tRNAscan – tRNA 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

http://www.tbi.univie.ac.at/~ivo/RNA/RNAfold.html
http://www.tbi.univie.ac.at/~ivo/RNA/RNAeval.html
http://www.tbi.univie.ac.at/~ivo/RNA/RNAheat.html
http://www.tbi.univie.ac.at/~ivo/RNA/RNAinverse.html
http://www.tbi.univie.ac.at/~ivo/RNA/RNAdistance.html
http://www.tbi.univie.ac.at/~ivo/RNA/RNApdist.html
Page 11: RNA Structure Prediction Rfam – RNA structures database RNAfold – RNA secondary structure prediction tRNAscan – tRNA prediction

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/

Page 12: RNA Structure Prediction Rfam – RNA structures database RNAfold – RNA secondary structure prediction tRNAscan – tRNA prediction

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).

Page 13: RNA Structure Prediction Rfam – RNA structures database RNAfold – RNA secondary structure prediction tRNAscan – tRNA prediction

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)

Page 14: RNA Structure Prediction Rfam – RNA structures database RNAfold – RNA secondary structure prediction tRNAscan – tRNA prediction

Sequence-Structure alignment

Free Energy

Enthalpy

Page 15: RNA Structure Prediction Rfam – RNA structures database RNAfold – RNA secondary structure prediction tRNAscan – tRNA prediction

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.

Page 16: RNA Structure Prediction Rfam – RNA structures database RNAfold – RNA secondary structure prediction tRNAscan – tRNA prediction

Graphic representation

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

Page 17: RNA Structure Prediction Rfam – RNA structures database RNAfold – RNA secondary structure prediction tRNAscan – tRNA prediction

RNAfold structure representations

Page 18: RNA Structure Prediction Rfam – RNA structures database RNAfold – RNA secondary structure prediction tRNAscan – tRNA prediction

tRNAscana program for detection of transfer RNA genes in genomic sequencehttp://lowelab.ucsc.edu/tRNAscan-SE/

It can process very long sequences

Page 19: RNA Structure Prediction Rfam – RNA structures database RNAfold – RNA secondary structure prediction tRNAscan – tRNA prediction
Page 20: RNA Structure Prediction Rfam – RNA structures database RNAfold – RNA secondary structure prediction tRNAscan – tRNA prediction
Page 21: RNA Structure Prediction Rfam – RNA structures database RNAfold – RNA secondary structure prediction tRNAscan – tRNA prediction

Non-coding RNA gene finding problems. Outline Introduction RNA secondary structure prediction RNA sequence-structure alignment

Folheto Natal Xavantes RFAM - irp-cdn.multiscreensite.com

C omputational ncRNA gene finding (& nc RNA structure prediction) Liming Cai (BINF8210@UGA, Fall 2010) nc RNA structure prediction (& computational ncRNA

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