Figure 1
Schematic flowchart of Cofolga2 algorithm. Cofolga2 algorithm is composed of three GA steps (initialization, evaluation, and reproduction) and a postprocessing step. In initialization, a population of individuals is randomly generated by weighted stochastic backtracking. In evaluation step, the objective function of each individual is evaluated and then fitness and selection probability are assigned to each individual. In reproduction, half of the population is replaced by new individuals to update the population. The iteration between evaluation and reproduction stops when one of the following conditions is satisfied: the best OF is not updated continuous Cmax times, or the number of iteration reaches a pre-defined maximum iteration number. The Cmax and the maximum iteration number are parameters given by user. A consensus secondary structure prediction for the optimal alignment is performed as a postprocessing, where the Nussinov matrix constructed by averaged base pairing probabilities is backtracked.