The input control file for running rnaga includes five lines data. For online users we provide a simple format in which only the first line needs to input. Other input data were set fixed and use default parameters.
1. File name that contains all sequences in a library format. The length of each sequence was limited less than 500 bp, and 50 sequences are maximum. However, the length of sequence (< 300 bp) and less than 10 sequences were recommanded. 2. Three input parameters: Hcrtval, Hcrtval2, and pns. The default values are (0.8, 0.7, 0.6). Hcrtval - If the conservation score for the structures is greater than Hcrtval the structures are considered as candidates of common structure during a GA iteration. Hcrtval2 - If the adjusted conservation score for the structure is greater than Hcrtval2 (Normally, Hcrtval2 < Hcrtval), the structure is taken as a common secondary structure. pns - A criterion to make sure that the structure feature in a common structure is shared by majority of the sequences (e.g. pns = 0.6 means that it is shared by at least 60% of the sequences). 3. Two integer values: The default values are (100, 100). The first integer is the total number of structures in a population and the other one is the total number of GA iterations. 4. Two parameters, beta and zeta: the criteria for the structure stability. beta - If the free energy of the structure is no greater than that (average random energy + beta * standard deviation) a structure is considered as a candidate during a GA iteration. zeta - If the free energy of the structure is no greater than that (average random energy + zeta * standard deviation) a structure is taken as a common structure. The default values are (1.0, 1.0). 5. Four integers for stem position, region size, loop size, and branches distance in determination of the equivalency of two compared stems in the different structures. The default values are (3,3,3,3).
Examples of Input Files: