Two algorithms for LCS Consecutive Suffix Alignment

Gad M. Landau, Eugene Myers, Michal Ziv-Ukelson

Research output: Contribution to journalArticlepeer-review

14 Scopus citations

Abstract

The problem of aligning two sequences A and B to determine their similarity is one of the fundamental problems in pattern matching. A challenging, basic variation of the sequence similarity problem is the incremental string comparison problem, denoted Consecutive Suffix Alignment, which is, given two strings A and B, to compute the alignment solution of each suffix of A versus B. Here, we present two solutions to the Consecutive Suffix Alignment Problem under the LCS (Longest Common Subsequence) metric, where the LCS metric measures the subsequence of maximal length common to A and B. The first solution is an O (n L) time and space algorithm for constant alphabets, where the size of the compared strings is O (n) and L ≤ n denotes the size of the LCS of A and B. The second solution is an O (n L + n log | Σ |) time and O (n) space algorithm for general alphabets, where Σ denotes the alphabet of the compared strings.

Original languageEnglish
Pages (from-to)1095-1117
Number of pages23
JournalJournal of Computer and System Sciences
Volume73
Issue number7
DOIs
StatePublished - 1 Jan 2007
Externally publishedYes

Keywords

  • Dynamic programming
  • Incremental algorithms
  • Longest common subsequence
  • Match point arithmetic

ASJC Scopus subject areas

  • Theoretical Computer Science
  • Computer Networks and Communications
  • Computational Theory and Mathematics
  • Applied Mathematics

Fingerprint

Dive into the research topics of 'Two algorithms for LCS Consecutive Suffix Alignment'. Together they form a unique fingerprint.

Cite this