The art of computer programming, volume 1 (3rd ed.): fundamental algorithms
The art of computer programming, volume 1 (3rd ed.): fundamental algorithms
Sequencing-by-hybridization at the information-theory bound: an optimal algorithm
RECOMB '00 Proceedings of the fourth annual international conference on Computational molecular biology
MFCS '94 Proceedings of the 19th International Symposium on Mathematical Foundations of Computer Science 1994
Reconstructing strings from substrings in rounds
FOCS '95 Proceedings of the 36th Annual Symposium on Foundations of Computer Science
Handling long targets and errors in sequencing by hybridization
Proceedings of the sixth annual international conference on Computational biology
Restricting SBH Ambiguity via Restriction Enzymes
WABI '02 Proceedings of the Second International Workshop on Algorithms in Bioinformatics
Restricting SBH ambiguity via restriction enzymes
Discrete Applied Mathematics
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Sequencing by hybridization (SBH) is a method for reconstructing a sequence over a small finite alphabet from a collection of probes (substrings). Substring queries can be arranged on an array (SBH chip) and then a combinatorial method is used to construct the sequence from its collection of probes. Technological constraints limit the number of substring queries that can be placed on a single SBH chip. We develop an idea of Margaritis and Skiena and propose an algorithm that uses a series of small SBH chips to sequence long strings while the number of probes used matches the information theoretical lower bound up to a constant factor.