Sequencing-by-hybridization at the information-theory bound: an optimal algorithm

Authors:
Franco P. Preparata;Eli Upfal
Affiliations:
Computer Science Department, Brown University, 115 Waterman Street, Providence, RI;Computer Science Department, Brown University, 115 Waterman Street, Providence, RI
Venue:
RECOMB '00 Proceedings of the fourth annual international conference on Computational molecular biology
Year:
2000

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Abstract

In a recent paper [PFU99) we have introduced a novel probing scheme for DNA sequencing by hybridization (SBH). The new gapped-probe scheme combines natural and universal bases in a well defined periodic pattern. It was shown in [PFU99] that the performance of the gapped-probe scheme (in terms of the length of a sequence that can be uniquely reconstructed using a given library size of probes) is significantly better than the standard scheme based on oligomer probes.In this paper we present and analyze a new, more powerful, sequencing algorithm for the gapped-probe scheme. We prove that the new algorithm exploits the full potential of the SBH technology with high-confidence performance, that comes within a small constant factor (about 2) of the information-theory bound. Moreover, this performance is achieved while maintaining running time linear in the target sequence length.