Sparse directed acyclic word graphs

Authors:
Shunsuke Inenaga;Masayuki Takeda
Affiliations:
Japan Society for the Promotion of Science;Department of Informatics, Kyushu University, Fukuoka, Japan
Venue:
SPIRE'06 Proceedings of the 13th international conference on String Processing and Information Retrieval
Year:
2006

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Abstract

The suffix tree of string w is a text indexing structure that represents all suffixes of w. A sparse suffix tree of w represents only a subset of suffixes of w. An application to sparse suffix trees is composite pattern discovery from biological sequences. In this paper, we introduce a new data structure named sparse directed acyclic word graphs (SDAWGs), which are a sparse text indexing version of directed acyclic word graphs (DAWGs) of Blumer et al. We show that the size of SDAWGs is linear in the length of w, and present an on-line linear-time construction algorithm for SDAWGs.