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

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Presentation on theme: "RNA Structure Prediction Rfam – RNA structures database RNAfold – RNA secondary structure prediction tRNAscan – tRNA prediction."— Presentation transcript:

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

2 Rfam Different search modes

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 Query Subject Structure Hit

6

7 :::::: free extremes ((())) Stem >> Internal Stem ______ Loop,,,,,, Internal loop Strucutre representaions

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9 Link to EMBL

10 RNA structure prediction Vienna RNA package: RNAfold predict minimum energy secondaryRNAfold structures and pair probabilities RNAalifold predict consensus secondary structureRNAalifold RNAeval evaluate energy of RNA secondaryRNAeval structures RNAheat calculate the specific heat (meltingRNAheat curve) of an RNA sequence RNAinverse inverse fold (design) sequences withRNAinverse predefined structure RNAdistance compare secondary structuresRNAdistance RNApdist compare base pair probabilitiesRNApdist RNAsubopt complete suboptimal foldingRNAsubopt

11 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/ http://www.tbi.univie.ac.at/~ivo/RNA/

12 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).

13 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)

14 Sequence-Structure alignment Free Energy Enthalpy

15 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.

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

17 RNAfold structure representations

18 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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