Languages of lossless seeds

Several algorithms for similarity search employ seeding techniques to quickly discard very dissimilar regions. In this paper, we study theoretical properties of lossless seeds, i.e., spaced seeds having full sensitivity. We prove that lossless seeds coincide with languages of certain sofic subshifts, hence they can be recognized by finite automata. Moreover, we show that these subshifts are fully given by the number of allowed errors k and the seed margin l. We also show that for a fixed k, optimal seeds must asymptotically satisfy l ~ m^(k/(k+1)).Comment: In Proceedings AFL 2014, arXiv:1405.527

The enumeration of three pattern classes using monotone grid classes

The structure of the three pattern classes defined by the sets of forbidden permutations \{2143,4321\}, \{2143,4312\} and \{1324,4312\} is determined using the machinery of monotone grid classes. This allows the permutations in these classes to be described in terms of simple diagrams and regular languages and, using this, the rational generating functions which enumerate these classes are determined