Solving the Molecular Sequence Alignment Problem with Generalized Differential Evolution 3 (GDE3)

Abstract

Molecular sequence alignment is one of the most essential tools of the molecular biology. It permits to track changes and similarities between molecular sequences. In this paper the molecular sequence alignment problem is formulated suitable for an evolutionary algorithm (EA), and two problem instances are solved using generalized differential evolution 3 (GDE3), which is a general purpose EA. Regardless of relatively large number of decision variables, the instances were solvable and results were comparable to those by sequence alignment solvers in comparison