Swiftly Computing Center Strings

Abstract

AbstractThe center string (or closest string) problem is a classical computer science problem with important applications in computational biology. Given k input strings and a distance threshold d, we search for a string within Hamming distance d to each input string. This problem is NP-complete. In this paper, we focus on exact methods for the problem that are also fast in application. First, we introduce data reduction techniques that allow us to infer that certain instances have no solution, or that a center string must satisfy certain conditions. Then, we describe a novel search tree strategy that is very efficient in practice. Finally, we present results of an evaluation study for instances from a biological application. We find that data reduction is mandatory for the notoriously difficult case d = d opt− 1.KeywordsSearch TreeClose StringBinary StringDistance ThresholdInput StringThese keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.