Property Suffix Array with Applications

  • Panagiotis Charalampopoulos
  • Costas S. Iliopoulos
  • Chang Liu
  • Solon P. Pissis
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 10807)

Abstract

The suffix array is one of the most prevalent data structures for string indexing; it stores the lexicographically sorted list of suffixes of a given string. Its practical advantage compared to the suffix tree is space efficiency. In Property Indexing, we are given a string x of length n and a property \(\varPi \), i.e. a set of \(\varPi \)-valid intervals over x. A suffix-tree-like index over these valid prefixes of suffixes of x can be built in time and space \(\mathcal {O}(n)\). We show here how to directly build a suffix-array-like index, the Property Suffix Array (PSA), in time and space \(\mathcal {O}(n)\). We mainly draw our motivation from weighted (probabilistic) sequences: sequences of probability distributions over a given alphabet. Given a probability threshold \(\frac{1}{z}\), we say that a string p of length m matches a weighted sequence X of length n at starting position i if the product of probabilities of the letters of p at positions \(i,\ldots ,i+m-1\) in X is at least \(\frac{1}{z}\). Our algorithm for building the PSA can be directly applied to build an \(\mathcal {O}(nz)\)-sized suffix-array-like index over X in time and space \(\mathcal {O}(nz)\).

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Copyright information

© Springer International Publishing AG, part of Springer Nature 2018

Authors and Affiliations

  • Panagiotis Charalampopoulos
    • 1
  • Costas S. Iliopoulos
    • 1
  • Chang Liu
    • 1
  • Solon P. Pissis
    • 1
  1. 1.Department of InformaticsKing’s College LondonLondonUK

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