String Indexing for Patterns with Wildcards

We consider the problem of indexing a string t of length n to report the occurrences of a query pattern p containing m characters and j wildcards. Let occ be the number of occurrences of p in t, and σ the size of the alphabet. We obtain the following results. A linear space index with query time O(m+σjloglog n+occ).

This significantly improves the previously best known linear space index by Lam et al. (in Proc. 18th ISAAC, pp. 846-857, [2007]), which requires query time Θ(jn) in the worst case. An index with query time O(m+j+occ) using space {Mathematical expression}, where k is the maximum number of wildcards allowed in the pattern.

This is the first non-trivial bound with this query time. A time-space trade-off, generalizing the index by Cole et al. (in Proc. 36th STOC, pp. 91-100, [2004]). We also show that these indexes can be generalized to allow variable length gaps in the pattern. Our results are obtained using a novel combination of well-known and new techniques, which could be of independent interest.