RNAGA: A program for predicting a secondary structure common to a number of phylogenetically related sequences without the need for pre-aligned RNA sequences. One of the remarkable features of RNAGA is that RNA secondary structures are automatically optimized by not only the free energy of the formation of the structure but also the structural similarity among homologous sequences.
The program operates in three stages. In the first stage, a genetic algorithm (GA) is used to generate a population of RNA secondary structures that satisfy certain conditions of thermodynamic stability. In this step, the free energy of a folded structure is taken as a fitness criterion. Secondly, we define a measure of structural conservation for the structure from one sequence with respect to those in other sequences. With this conservation measure as the fitness criterion, GA is then used to improve the structural similarity among homologous RNAs for the structures in the population of a sequence. Finally, those structures that satisfy certain conditions of thermodynamic stability and structural conservation are selected as predicted common structures for a set of homologous RNAs.
These predictions are ranked in descending order based on the structural conservation score. The program is based on the genetic algorithm and implemented in Fortran 90 running on Unix.
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