Linear pattern matching on sparse suffix trees

Packing several characters into one computer word is a simple and natural way to compress the representation of a string and to speed up its processing. Exploiting this idea, we propose an index for a packed string, based on a sparse suffix tree [8] with appropriately defined suffix links. Assuming, under the standard unit-cost RAM model, that a word can store up to logσ n characters (σ the alphabet size), our index takes O(n/ logσ n) space, i.e. the same space as the packed string itself. The resulting pattern matching algorithm runs in time O(m + r + r · occ), where m is the length of the pattern, r is the actual number of characters stored in a word and occ is the number of pattern occurrences.