Sparse Suffix Tree Construction with Small Space

Sparse Suffix Tree Construction in Small Space

Sparse Suffix Tree Construction in Optimal Time and Space

Suffix tree (and the closely related suffix array) are fundamental structures capturing all substrings of a given text essentially by storing all its suffixes in the lexicographical order. In some applications, such as sparse text indexing, we work with a subset of b interesting suffixes, which are stored in the so-called sparse suffix tree. Because the size of this structure is Θ(b), it is nat...

Optimal Substring-Equality Queries with Applications to Sparse Text Indexing

We consider the problem of encoding a string of length n from an alphabet [0, σ − 1] so that access and substring-equality queries (that is, determining the equality of any two substrings) can be answered efficiently. A clear lower bound on the size of any prefix-free encoding of this kind is n log σ + Θ(log(nσ)) bits. We describe a new encoding matching this lower bound when σ ≤ nO(1) while su...

On-Line Linear-Time Construction of Word Suffix Trees

Suffix trees are the key data structure for text string matching, and are used in wide application areas such as bioinformatics and data compression. Sparse suffix trees are kind of suffix trees that represent only a subset of suffixes of the input string. In this paper we study word suffix trees, which are one variation of sparse suffix trees. Let D be a dictionary of words and w be a string i...

Sparse compact directed acyclic word graphs

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 analy...