The program RNAGA is capable to produce consensus secondary structures of homologous RNA sequences from the primary sequences information only. The method does not require structural information nor alignment information. The method is computationally demanding. The program is being actively evolved.
The program RNAGA package includes following files:
1. RNAGA Source Codes: ga.f - source code for 'main' and other routines including the routine that computes the conservation score for each structure. gtstr.f - source code for generating the inial population of structures mga.f - miscellaneous subroutines mutat.f - source code for the mutation operation xovr.f - source code for the crossover operation gtmseq.f - source code to read multiple sequences efn.f - source code to compute the energy (Zuker's dynamic programming algorithm) gtrerg.f - source code to compute the average random energy and its standard deviation based on the base composition It can be easily compiled by f77 -o rnaga ga.f gtstr.f mga.f mutat.f xovr.f gtmseq.f efn.f gtrerg.f 2. Energy Data Files for RNAGA: ergparm - Turner energy rules for RNA folding) cf20, cf30, cf50, cf100, and cf150 (Five files containing empiracal energy coefficientsare are used to computer sample mean and standard deviation, respectively, of the lowest free energies from randomly shuffled sequences based on the size and base compositions of the random sequences. The computed values are compatible with that computed directly by Turner energy rules. 3. Test Data Files: Sequence file: rnaga.seq Input control file: rnaga.in Output files: main output is rnaga.cm (a *cm file). It contains the predicted common secondary structures. The structure is represented as a set of stems. The rnaga.scr (a *scr file) is the other output. It contains the detailed similarity scores among these predictions computed in the different cycle.