Matching statistics were introduced to solve the approximate string matching problem, which is a recurrent subroutine in bioinformatics applications. In 2010, Ohlebusch et al. [SPIRE 2010] proposed a time and space efficient algorithm for computing matching statistics which relies on some components of a compressed suffix tree-notably, the longest common prefix (LCP) array. In this paper, we show how their algorithm can be generalized from strings to Wheeler deterministic finite automata. Most importantly, we introduce a notion of LCP array for Wheeler automata, thus establishing a first clear step towards extending (compressed) suffix tree functionalities to labeled graphs.
Computing matching statistics on Wheeler DFAs
Cotumaccio, Nicola;Gagie, Travis;Manzini, Giovanni;Prezza, Nicola;
2023-01-01
Abstract
Matching statistics were introduced to solve the approximate string matching problem, which is a recurrent subroutine in bioinformatics applications. In 2010, Ohlebusch et al. [SPIRE 2010] proposed a time and space efficient algorithm for computing matching statistics which relies on some components of a compressed suffix tree-notably, the longest common prefix (LCP) array. In this paper, we show how their algorithm can be generalized from strings to Wheeler deterministic finite automata. Most importantly, we introduce a notion of LCP array for Wheeler automata, thus establishing a first clear step towards extending (compressed) suffix tree functionalities to labeled graphs.File | Dimensione | Formato | |
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