Efficient algorithm for testing structure freeness of finite set of biomolecular sequences

Abstract

In this paper we will focus on the structure freeness test problem of finite sets of sequences. The result is an extension of Andronescu's algorithm which can be applied to the sequence design of various DNA computing experiments. We will first give a general algorithm for this problem which runs in O(n5) time. Then, we will give an evaluation method for sequence design system, which requires O(n5) time for precomputation, and O(n4) time and O(n5) space for each evaluation of sequence sets. The authors believe that this result will give an important progress of efficient sequence design systems. © Springer-Verlag Berlin Heidelberg 2006.