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You are here: Foswiki>ABI Web>ResearchLogEnricoSiragusa>SeedDesign (25 Nov 2010, EnricoSiragusa)Edit Attach
Page SeedDesign
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.- Optimal Threshold Computation for Non-Gapped Seeds
- Optimal Threshold Computation for Seeds
- Optimal Threshold Computation for Families of Seeds
- Filter Analysis for Families of Seeds
- Hit Probability Computation for Seeds
- Hit Probability Computation for Families of Seeds
- Overlap Complexity Computation for Families of Seeds
- Hardness Results
- Comments
Optimal Threshold Computation for Non-Gapped Seeds
Ukkonen paper. q-Gram lemma.Optimal Threshold Computation for Seeds
Burkhardt and Kaerkkaeinen paper. FPT algorithm. Bounding criterion.Optimal Threshold Computation for Families of Seeds
Kucherov, Noe and Rotyberg paper. FPT algorithms. Expansion and Contraction. Periodicity.Filter Analysis for Families of Seeds
Fontaine, Burkhardt and Kaerkkaeinen paper. BDDs.Hit Probability Computation for Seeds
Keich, Li, Ma and Tromp paper. KLMT algorithm.Hit Probability Computation for Families of Seeds
Li, Ma and Tromp paper. PatternHunterII.Overlap Complexity Computation for Families of Seeds
Ilie and Ilie paper.Hardness Results
Nicolas and Rivals paper. Keich, Li, Ma and Tromp paper. Kaerkkaeinen paper.Comments
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Topic revision: r2 - 25 Nov 2010, EnricoSiragusa
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