Restricting SBH Ambiguity via Restriction Enzymes
WABI '02 Proceedings of the Second International Workshop on Algorithms in Bioinformatics
Reconstructing strings from substrings in rounds
FOCS '95 Proceedings of the 36th Annual Symposium on Foundations of Computer Science
Sequencing-by-Hybridization Revisited: The Analog-Spectrum Proposal
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Optimal probing patterns for sequencing by hybridization
WABI'06 Proceedings of the 6th international conference on Algorithms in Bioinformatics
Tight bounds for string reconstruction using substring queries
APPROX'05/RANDOM'05 Proceedings of the 8th international workshop on Approximation, Randomization and Combinatorial Optimization Problems, and Proceedings of the 9th international conference on Randamization and Computation: algorithms and techniques
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Sequencing by Hybridization (SBH) is a method for reconstructing an unknown DNA string based on obtaining, through hybridization experiments, whether certain short strings appear in the target string. Following Margaritis and Skiena (1995) [12], we study the SBH in rounds problem: The goal is to reconstruct an unknown string A (over a fixed alphabet) using queries of the form ''does the string S appear in A?'' for some query string S. The queries are performed in rounds, where the queries in each round depend on the answers to the queries in the previous rounds. We show that almost all strings of length n can be reconstructed in log^*n rounds with O(n) queries per round. We also consider a variant of the problem in which for each substring query S, the answer is whether S appears once in the string A, appears at least twice in A, or does not appear in A. For this problem, we show that almost all strings can be reconstructed in 2 rounds of O(n) queries. Our results improve the previous results of Margaritis and Skiena (1995) [12] and Frieze and Halldorsson (2002) [8].