Testing structure freeness of regular sets of biomolecular sequences

Abstract

p x → q This paper discusses a problem of checking the structure freeness of DNA and RNA sequences. A set R of sequences over ∑ is said to be structure free if for every α ε R, the minimum free energy of α is greater than or equal to 0. It was open whether or not there exists a polynomial time algorithm for testing the structure freeness of a given regular set R. In this paper, we will solve this problem. © Springer-Verlag Berlin Heidelberg 2005.