Efficient Non-Coding RNA Gene Searches Through Classical and Evolutionary Methods
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.
Smith, Jennifer A.. (2008). "Efficient Non-Coding RNA Gene Searches Through Classical and Evolutionary Methods". International Journal of Computational Intelligence in Bioinformatics and Systems Biology, 1(1), 42-58. http://dx.doi.org/10.1504/IJCIBSB.2009.024043