A fast genetic algorithm for RNA secondary structure analysis

A fast genetic algorithm GArna for mass calculations of RNA secondary structures through the Internet is proposed. The algorithm GArna was used to study the effects of nucleotide composition on characteristics of the secondary structure of random RNA sequences. A contextual characteristics for evaluation of the stability was proposed and the application of standard statistical tests for heterogeneous RNA samplings was justified. The structure-contextual characteristics by which the 5"-untranslated regions of high- and low-expression genes of dicot plants and mammals differ were found, and the results were interpreted in terms of secondary structure influence on translation initiation and on the general scheme of expression regulation. The application of the results obtained for the development of computer methods for RNA structural genomics, in particular, for RNA search in genome sequences, is discussed.