Efficient seed computation revisited

M. Christou, M. Crochemore, C. S. Iliopoulos, M. Kubica, S. P. Pissis, J. Radoszewski*, W. Rytter, B. Szreder, T. Waleń

*Corresponding author for this work

Research output: Contribution to JournalArticleAcademicpeer-review

Abstract

The notion of the cover is a generalization of a period of a string, and there are linear time algorithms for finding the shortest cover. The seed is a more complicated generalization of periodicity, it is a cover of a superstring of a given string, and the shortest seed problem is of much higher algorithmic difficulty. The problem is not well understood, no linear time algorithm is known. In the paper we give linear time algorithms for some of its versions - computing shortest left-seed array, longest left-seed array and checking for seeds of a given length. The algorithm for the last problem is used to compute the seed array of a string (i.e., the shortest seeds for all the prefixes of the string) in O(n2) time. We describe also a simpler alternative algorithm computing efficiently the shortest seeds. As a by-product we obtain an O(nlog(n/m)) time algorithm checking if the shortest seed has length at least m and finding the corresponding seed. We also correct some important details missing in the previously known shortest-seed algorithm Iliopoulos et al. (1996) [14].

Original languageEnglish
Pages (from-to)171-181
Number of pages11
JournalTheoretical Computer Science
Volume483
DOIs
Publication statusPublished - 29 Apr 2013
Externally publishedYes

Keywords

  • Cover
  • Seed in a string
  • Suffix tree

Fingerprint

Dive into the research topics of 'Efficient seed computation revisited'. Together they form a unique fingerprint.

Cite this