A KINETIC-MODEL OF RNA FOLDING

The RNA folding process is represented as a Markov process with states corresponding to RNA secondary structures and transition probabilitie s corresponding to transformations of a secondary structure caused by formation or disintegration of a helix. Transition probabilities (kine tic constants) are determined. A notion of a group of structures is in troduced, and it allows to reduce the state space. Energetic and kinet ic parameters of pseudoknots are estimated. Algorithms for computation of a kinetic ensemble for structures and groups of structures are pre sented, as well as their modifications that take into account pseudokn ots. The described algorithms are implemented as a procedure for predi ction of RNA secondary structure that is included in the package DNA-S UN.