On the power of universal bases in sequencing by hybridization
RECOMB '99 Proceedings of the third annual international conference on Computational molecular biology
MFCS '94 Proceedings of the 19th International Symposium on Mathematical Foundations of Computer Science 1994
Enhanced Sequence Reconstruction with DNA Microarray Application
COCOON '01 Proceedings of the 7th Annual International Conference on Computing and Combinatorics
Accelerating DNA sequencing-by-hybridization with noise
Proceedings of the 5th international workshop on Bioinformatics
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DNA sequencing-by-hybridization (SBH) is a powerful potential alternative to current sequencing by electrophoresis. Different SBH methods have been compared under the hypothesis of error-free hybridization. However both false negatives and false positive are likely to occur in practice. Under the assumption of random independent hybridization errors, Doi and Imai [3] recently concluded that the algorithms of [15], which are asymptotically optimal in the error-free case, cannot be successfully adapted to noisy conditions. In this paper we prove that the reported dramatic drop in performance is attributable to algorithmic artifacts, and present instead an algorithm for sequence reconstruction under hybridization noise, which exhibits graceful degradation of performance as the error-rate increases. As a downside, the computational cost of sequence reconstruction rises noticeably under noisy conditions.