Resequencing a Set of Strings Based on a Target String

Resequencing a Set of Strings Based on a Target String

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Article ID: iaor201526345
Volume: 72
Issue: 2
Start Page Number: 430
End Page Number: 449
Publication Date: Jun 2015
Journal: Algorithmica
Authors: , , ,
Keywords: sequencing, text processing, subsequence
Abstract:

Given a set S={S 1,S 2,…,S l } of l strings, a text T, and a natural number k, find a string M, which is a concatenation of k strings (not necessarily distinct, i.e., a string in S may occur more than once in M) from S, whose longest common subsequence with T is largest, where a string in S may occur more than once in M. Such a string is called a k‐inlay. The resequencing longest common subsequence problem (resequencing LCS problem for short) is to find a k‐inlay for each query with parameter k after T and S are given. In this paper, we propose an algorithm for solving this problem which takes O(nml) preprocessing time and O(ϑ k k) query time for each query with parameter k, where n is the length of T, m is the maximal length of strings in S, and ϑ k is the length of the longest common subsequence between a k‐inlay and T.

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