Single and multiple consecutive permutation motif search
Abstract
Let be a permutation (that shall play the role of the {\em text}) on and a pattern be a sequence of distinct integer(s) of , . The pattern occurs in in position if and only if is order-isomorphic to , that is, for all , if and only if . Searching for a pattern in a text consists in identifying all occurrences of in . We first present a forward automaton which allows us to search for in in time. We then introduce a Morris-Pratt automaton representation of the forward automaton which allows us to reduce this complexity to at the price of an additional amortized constant term by integer of the text. Both automata occupy space. We then extend the problem to search for a set of patterns and exhibit a specific Aho-Corasick like algorithm. Next we present a sub-linear average case search algorithm running in time, that we eventually prove to be optimal on average.
Keywords
Cite
@article{arxiv.1301.4952,
title = {Single and multiple consecutive permutation motif search},
author = {Djamal Belazzougui and Adeline Pierrot and Mathieu Raffinot and Stéphane Vialette},
journal= {arXiv preprint arXiv:1301.4952},
year = {2013}
}