TY - JOUR

T1 - Parameterized complexity analysis for the Closest String with Wildcards problem

AU - Hermelin, Danny

AU - Rozenberg, Liat

N1 - Publisher Copyright:
© 2015 Elsevier B.V.

PY - 2015/10/4

Y1 - 2015/10/4

N2 - The Closest String problem asks to find a string s which is not too far from each string in a set of m input strings, where the distance is taken as the Hamming distance. This well-studied problem has various applications in computational biology and drug design. In this paper, we introduce a new variant of Closest String where the input strings can contain wildcards that can match any letter in the alphabet, and the goal is to find a solution string without wildcards. We call this problem the Closest String with Wildcards problem, and we analyze it in the framework of parameterized complexity. Our study determines for each natural parameterization whether this parameterization yields a fixed-parameter algorithm, or whether such an algorithm is highly unlikely to exist.

AB - The Closest String problem asks to find a string s which is not too far from each string in a set of m input strings, where the distance is taken as the Hamming distance. This well-studied problem has various applications in computational biology and drug design. In this paper, we introduce a new variant of Closest String where the input strings can contain wildcards that can match any letter in the alphabet, and the goal is to find a solution string without wildcards. We call this problem the Closest String with Wildcards problem, and we analyze it in the framework of parameterized complexity. Our study determines for each natural parameterization whether this parameterization yields a fixed-parameter algorithm, or whether such an algorithm is highly unlikely to exist.

KW - Computational biology

KW - Fixed-parameter algorithms

KW - Parameterized complexity

KW - The closest string problem

UR - http://www.scopus.com/inward/record.url?scp=84941260466&partnerID=8YFLogxK

U2 - 10.1016/j.tcs.2015.06.043

DO - 10.1016/j.tcs.2015.06.043

M3 - Article

AN - SCOPUS:84941260466

VL - 600

SP - 11

EP - 18

JO - Theoretical Computer Science

JF - Theoretical Computer Science

SN - 0304-3975

ER -