This page contains an essay on the state of the art of seed design. The goal of this essay is to give an unifying view on seed design. Most relevant papers on seed design are summarized here.
Ukkonen paper. q-Gram lemma.
Burkhardt and Kaerkkaeinen paper. FPT algorithm. Bounding criterion.
Kucherov, Noe and Rotyberg paper. FPT algorithms. Expansion and Contraction. Periodicity.
Fontaine, Burkhardt and Kaerkkaeinen paper. BDDs.
Keich, Li, Ma and Tromp paper. KLMT algorithm.
Li, Ma and Tromp paper. PatternHunterII.
Ilie and Ilie paper.
Nicolas and Rivals paper. Keich, Li, Ma and Tromp paper. Kaerkkaeinen paper.