Covarying mutations

RNAalifold, a popular computational method for RNA consensus structure prediction, incorporates covarying mutations into a thermodynamic model to fold the aligned RNA sequences. When quantifying covariance, it evaluates conserved signals of two aligned columns with base-pairing rules.

10p viwyoming2711 16-12-2020 10 1   Download

This paper relies on the idea that a proper search operator, which captures mentioned implicit correlations, can improve performance of evolutionary constrained optimization algorithms. To realize this, an Evolution Strategy (ES) along with a simplified Covariance Matrix Adaptation (CMA) based mutation operator is used with a ranking based constraint-handling method. The proposed algorithm is tested on 13 benchmark problems as well as on a real life design problem.

13p vinguyentuongdanh 19-12-2018 6 0   Download