Alan M. Frieze
ABSTRACT
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.
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Index Terms
- Optimal sequencing by hybridization in rounds
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