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

3 Browse Rfam

4

5 Search Rfam

6 Query Subject Structure Hit

7

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

9 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

10 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/

11 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).

12 Input sequence Fold Algorithm: partition function recomended Output formats

13 Sequence-Structure alignment Free Energy

14 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. Minimal total base- pair distance

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

16 RNAfold structure representations

17 tRNAscan a program for detection of transfer RNA genes in genomic sequence http://lowelab.ucsc.edu/tRNAscan-SE/

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