HierarchyScan: a hierarchical similarity search algorithm for databases of long sequences

We present a hierarchical algorithm, HierarchyScan, that efficiently locates one-dimensional subsequences within a collection of sequences of arbitrary length. The subsequences identified by HierarchyScan match a given template pattern in a scale- and phase-independent fashion. The idea is to perform correlation between the stored sequences and the template in the transformed domain hierarchically. Only those subsequences whose maximum correlation value is higher than a predefined threshold will be selected. The performance of this approach is compared to the sequential scanning and an order-of-magnitude speedup is observed.