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RNA Structure Prediction

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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RNA Structure Prediction

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

  2. Rfam Different search modes http://rfam.sanger.ac.uk/

  3. 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

  4. Search Rfam

  5. Hit Structure Subject Query

  6. Strucutre representaions :::::: free extremes ((())) Stem <<<>>> Internal Stem ______ Loop ,,,,,, Internal loop

  7. Link to EMBL

  8. 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

  9. 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/

  10. 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).

  11. 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

  12. Sequence-Structure alignment Free Energy Enthalpy

  13. 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

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

  15. RNAfold structure representations

  16. tRNAscan a program for detection of transfer RNA genes in genomic sequence http://lowelab.ucsc.edu/tRNAscan-SE/ It can process very long sequences

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