Dotted suffix trees a structure for approximate text indexing

Abstract

In this work, the problem we address is text indexing for approximate matching. Given a text τ which undergoes some preprocessing to generate an index, we can later query this index to identify the places where a string occurs up to a certain number of errors k (edition distance). The indexing structure occupies space O(n logk n) in the average case, independent of alphabet size. This structure can be used to report the existence of a match with k errors in O(3kmk+1) and to report the occurrences in O(3kmk+1 + ed) time, where m is the length of the pattern and ed and the number of matching edit scripts. The construction of the structure has time bound by O(kN|Σ|), where N is the number of nodes in the index and |Σ| the alphabet size. © Springer-Verlag Berlin Heidelberg 2006.