Bests hits of 11110110111: i.i.d model-free and parameter-free calculation of spaced seed sensitivity

Dominant seeds have been introduced by Mak and Benson (2009) in order to reduce the number of candidate seeds and to allow parameter-free calculation of spaced seed sensitivity. We extend their work on the Bernoulli model by considering the Hit Integration, the Heaviside and the Dirac models, and the design of multiple seeds. From a theoretical standpoint, we show that a simple general framework can be set on these models by use of a counting semi-ring. From a practical standpoint, we experimentally confirm that dominant seeds reduce the set of seeds, either to explore for single seeds, otherwise to store for multiple seeds, and give i