Text Indexing and Dictionary Matching with One Error

Abstract

The indexing problem is where a text is preprocessed and subsequent queries of the form "Find all occurrences of pattern P in the text" are answered in time proportional to the length of the query and the number of occurrences. In the dictionary matching problem a set of patterns is preprocessed and subsequent queries of the form "Find all occurrences of dictionary patterns in text T" are answered in time proportional to the length of the text and the number of occurrences. There exist efficient worst-case solutions for the indexing problem and the dictionary matching problem, but none that find approximate occurrences of the patterns, i.e., where the pattern is within a bound edit (or Hamming) distance from the appropriate text location. In this paper we present a uniform deterministic solution to both the indexing and the general dictionary matching problem with one error. We preprocess the data in time O(n log2 n), where n is the text size in the indexing problem and the dictionary size in the dictionary matching problem. Our query time for the indexing problem is O(m log n log log n + tocc), where m is the query string size and tocc is the number of occurrences. Our query time for the dictionary matching problem is O(n log3 d log log d + tocc), where n is the text size and d the dictionary size. The time bounds above apply to both bounded and unbounded alphabets. © 2000 Academic Press.