Closest String and Substring Problems

Abstract

The problem of finding a center string that is `close' to every given string arises and has many applications in computational biology and coding theory. This problem has two versions: the Closest String problem and the Closest Substring problem. Assume that we are given a set of strings ${\cal S}=\{s_1, s_2, ..., s_n\}$ of strings, say, each of length $m$. The Closest String problem asks for the smallest $d$ and a string $s$ of length $m$ which is within Hamming distance $d$ to each $s_i\in {\cal S}$. This problem comes from coding theory when we are looking for a code not too far away from a given set of codes. The problem is NP-hard. Berman et al give a polynomial time algorithm for constant $d$. For super-logarithmic $d$, Ben-Dor et al give an efficient approximation algorithm using linear program relaxation technique. The best polynomial time approximation has ratio 4/3 for all $d$ given by Lanctot et al and Gasieniec et al. The Closest Substring problem looks for a string $t$ which is within Hamming distance $d$ away from a substring of each $s_i$. This problem only has a $2- \frac{2}{2|\Sigma|+1}$ approximation algorithm previously Lanctot et al and is much more elusive than the Closest String problem, but it has many applications in finding conserved regions, genetic drug target identification, and genetic probes in molecular biology. Whether there are efficient approximation algorithms for both problems are major open questions in this area. We present two polynomial time approxmation algorithms with approximation ratio $1+ \epsilon$ for any small $\epsilon$ to settle both questions.