In this paper we study the structure of suffix trees. Given an unlabeled tree τ on n nodes and suffix links of its internal nodes, we ask the question “Is τ a suffix tree?”, i.e., is there a string S whose suffix tree has the same topological structure as τ? We place no restrictions on S, in particular we do not require that S ends with a unique symbol. This corresponds to considering the more ...

SYNONYMS Compact suffix trie DEFINITION The suffix tree S(y) of a non-empty string y of length n is a compact trie representing all the suffixes of the string. The suffix tree of y is defined by the following properties: All branches of S(y) are labeled by all suffixes of y. • • Edges of S(y) are labeled by strings. • Internal nodes of S(y) have at least two children. • Edges outgoing an intern...

The structural match (s-match), originally addressed by the structural suffix tree, helps identify different RNA sequences with the same secondary structure. In this work, we introduce and construct the structural suffix array and structural longest common prefix array, i.e. lightweight suffix data structures for the s-match. Further, we illustrate how to use our data structures to support addi...

Suppose we have a large dictionary of strings. Each entry starts with a figure of merit (popularity). We wish to find the kbest matches for a substring, s, in a dictinoary, dict. That is, grep s dict | sort –n | head –k, but we would like to do this in sublinear time. Example applications: (1) web queries with popularities, (2) products with prices and (3) ads with click through rates. This pap...

Exact string matching is a problem that computer programmers face on a regular basis, and full-text indexes like the suffix tree or the suffix array provide fast string search over large texts. In the last decade, research on compressed indexes has flourished because the main problem in large-scale applications is the space consumption of the index. Nowadays, the most successful compressed inde...

Given string S[1..N ] and integer k, the suffix selection problem is to determine the kth lexicographically smallest amongst the suffixes S[i . . . N ], 1 ≤ i ≤ N . We study the suffix selection problem in the cache-aware model that captures two-level memory inherent in computing systems, for a cache of limited size M and block size B. The complexity of interest is the number of block transfers...

Using the suffix tree of a string S, decision queries of the type “Is P a substring of S?” can be answered in O(|P |) time and enumeration queries of the type “Where are all z occurrences of P in S?” can be answered in O(|P |+z) time, totally independent of the size of S. However, in large scale applications as genome analysis, the space requirements of the suffix tree are a severe drawback. Th...

Our production experiment in Scottish English revealed that the duration of a rhyme immediately followed by a Level II suffix such as –s (the 1 person singular/plural/possessive suffix) and –t (the past tense suffix) was significantly longer than that of a monomorphemic counterpart. Such a durational difference between suffixed forms and monomorphemic forms was absent when the Level II suffix w...

Suffix automata and factor automata are efficient data structures for representing the full index of a set of strings. They are minimal deterministic automata representing the set of all suffixes or substrings of a set of strings. This paper presents a novel analysis of the size of the suffix automaton or factor automaton of a set of strings. It shows that the suffix automaton or factor automat...

The inflectional thesaurus is a tool which (1) first performs the morphological segmentation of the input wordform, then (2) finds its stem's lexical base(s), (3) stores the suffix sequence situated on the right of the actual stem-allomorph, (4) offers the synonyms for the lexical base(s), and (5) generates the new word-form consisting of the adequate allomorph of the chosen stem and the adequa...