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A Modification of the Landau-Vishkin Algorithm Computing Longest Common

Summary: A Modification of the Landau-Vishkin
Algorithm Computing Longest Common
Extensions via Suffix Arrays
Rodrigo de Castro Miranda1
and Mauricio Ayala-Rinc´on1
Mestrado em Inform´atica e Departamento de Matem´atica, Universidade de Bras´ilia,
Abstract. Approximate string matching is an essential problem in many
areas related to Computer Science including biological sequence process-
ing. The standard solution of this problem is an O(mn) running time and
space dynamic programming algorithm for two strings of length m and
n. Landau and Vishkin developed an algorithm which uses suffix trees
for accelerating the computation along the dynamic programming table
and reaching space and running time in O(nk), where n > m and k is the
maximum number of admissible differences. Suffix trees are used for pre-
processing the sequences allowing an O(1) running time computation of
the longest common extensions between substrings. One of the practical
drawbacks of the Landau-Vishkin algorithm is the excessive use of space
inherent to the use of suffix trees. In fact, although suffix trees can be


Source: Ayala-Rincón, Mauricio - Departamento de Matemática, Universidade de Brasília


Collections: Mathematics