EPR-dictionaries: A practical and fast data structure for constant time searches in unidirectional and bidirectional FM-indices

Abstract

We introduce a new, practical method for conducting an exact search in a uni- and bidirectional FM index in $O(1)$ time per step while using $O(\log \sigma \ast n)+o(\log \sigma \ast \sigma \ast n)$ bits of space. This is done by replacing the binary wavelet tree by a new data structure, the Enhanced Prefixsum Rank dictionary (EPR-dictionary). We implemented this method in the SeqAn C++ library and experimentally validated our theoretical results. In addition we compared our implementation with other freely available implementations of bidirectional indices and show that we are between $\approx 2.6-4.8$ times faster. This will have a large impact for many bioinformatics applications that rely on practical implementations of (2)FM indices e.g. for read mapping. To our knowledge this is the first implementation of a constant time method for a search step in 2FM indices.