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giovedì, 21 settembre 2023


Dettagli Pubblicazione
Autori:Lavinia Egidi
Giovanni Manzini
Area Scientifica:Bioinformatics
Titolo:Spaced Seeds Design Using Perfect Rulers
Apparso su:TR-INF-2011-06-01-UNIPMN
Editore:Computer Science Department, UPO
Tipo Pubblicazione:Technical Report
Sommario: We consider the problem of lossless spaced seed design for approximate pattern matching. We show that, using mathematical objects known as perfect rulers, we can derive a family of spaced seeds for matching with up to two errors. We analyze these seeds with respect to the trade-off they offer between seed weight and the minimum length of the pattern to be matched. We prove that for patterns of length up to a few hundreds our seeds have a larger weight, hence a better filtration efficiency, than the ones known in the literature. In this context, we study in depth the specific case of Wichmann rulers and prove some preliminary results on the generalization of our approach to the larger class of unrestricted rulers.