Indexed Hierarchical Approximate String Matching

We preset a new search procedure for approximate string matching over suffix trees. We show that hierarchical verification, which is a well-established technique for on-line searching, can also be used with an indexed approach. For this, we need that the index supports bidirectionality, meaning that the search for a pattern can be updated by adding a letter at the right or at the left. This turns out to be cosily supported by most compressed text self-indexes, which represent the index and the text essentially in the salve space of the compressed text alone. To complete the symbiotic exchange; our hierarchical verification largely reduces the need to access the text, which is expensive in compressed text self-indexes. The resulting algorithm can, in particular, run over an existing fully compressed suffix tree; which makes it very appealing for applications in computational biology. We compare our algorithm with related approaches; showing that our method offers an interesting space/time tradeoff, and in particular does slot need of any parameterization, which is necessary in the most successful competing approaches.