The Prague Stringology Conference 2006

Shunsuke Inenaga and Masayuki Takeda

Sparse Compact Directed Acyclic Word Graphs

Abstract:
The suffix tree of string w represents all suffixes of w, and thus it supports full indexing of w for exact pattern matching. On the other hand, a sparse suffix tree of w represents only a subset of the suffixes of w, and therefore it supports sparse indexing of w. There has been a wide range of applications of sparse suffix trees, e.g., natural language processing and biological sequence analysis. Word suffix trees are a variant of sparse suffix trees that are defined for strings that contain a special word delimiter #. Namely, the word suffix tree of string w = w1w2...wk, consisting of k words each ending with #, represents only the k suffixes of w of the form wi...wk. Namely, the word suffix tree of string w = w1w2...wk, consisting of k words each ending with #, represents only the k suffixes of w of the form wi...wk. Recently, we presented an algorithm which builds word suffix trees in O(n) time with O(k) space, where n is the length of w. In addition, we proposed sparse directed acyclic word graphs (SDAWGs) and an on-line algorithm for constructing them, working in O(n) time and space. As a further achievement of this research direction, this paper introduces yet a new text indexing structure named sparse compact directed acyclic word graphs (SCDAWGs). We show that the size of SCDAWGs is smaller than that of word suffix trees and SDAWGs, and present an SCDAWG construction algorithm that works in O(n) time with O(k) space and in an on-line manner.

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