Efficient non-coding RNA gene searches through classical and evolutionary methods

Abstract

Successful non-coding RNA gene searching requires examination of long-range intramolecular base pairing possibilities. This results in search algorithms with extremely long run times such that large-scale use of the algorithms often becomes computationally infeasible. Methods for the efficient search of the solution space are examined. A review of the standard dynamic-programming covariance model search algorithm is given. An analysis of the statistically probable regions of the search space is undertaken and a method of limiting the traditional dynamic-programming algorithm to this region is shown. An alternative search method using a Genetic Algorithm (GA) which favours the probable region of the search space is also given.