Prediction of 3D Structure (Folding) of a RNA Sequence

RNA Structure

Ribonucleic acid (RNA) is a linear single-stranded molecule that takes part in translation to protein. The intramolecular interactions (a.k.a. folding) of RNA base pairs (A=U and C≡G) form a secondary structure. Nussinov (or) Zuker algorithm is a dynamic programming approach used for the prediction of the secondary structure of the RNA. The dot-bracket structure with the minimum free energy is a stable secondary structure.

Prediction of the three-dimensional (3D) structure of RNA using mFold and RNAComposer tools have demonstrated in this tutorial. The mFold tool predicts the dot-bracket notation format RNA folding result from the RNA sequence, while the RNAComposer tool predicts the 3D structure from the dot-bracket notation. The resources used in this tutorial are NCBI GenBank, mFold, and RNAComposer.

Note: The length of RNA sequence input in mFold is limited to 4000 bases and sequence/dot-bracket notation input in RNAComposer is limited to 500 bases, due to the complexity of the algorithm used in the programs.

Comments

Most Popular Posts

Technical Questions

RNA to Protein Translation in PERL

Simple Server and Client Chat using Python