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Bioinformatics Vol. 17 no. 10 2001
Pages 862-870
© 2001 Oxford University Press

Dealing with errors in interactive sequencing by hybridization

Vinhthuy T. Phan and Steven S. Skiena

Department of Computer Science, State University of New York, Stony Brook, NY 11794-4400, USA

Received on April 20, 2001 ; revised on July 2, 2001 ; accepted on July 2, 2001

Motivation: A realistic approach to sequencing by hybridization must deal with realistic sequencing errors. The results of such a method can surely be applied to similar sequencing tasks.

Results: We provide the first algorithms for interactive sequencing by hybridization which are robust in the presence of hybridization errors. Under a strong error model allowing both positive and negative hybridization errors without repeated queries, we demonstrate accurate and efficient reconstruction with error rates up to 7%. Under the weaker traditional error model of Shamir and Tsur (Proceedings of the Fifth International Conference on Computational Molecular Biology (RECOMB-01) , pp 269–277, 2000), we obtain accurate reconstructions with up to 20% false negative hybridization errors. Finally, we establish theoretical bounds on the performance of the sequential probing algorithm of Skiena and Sundaram (J. Comput. Biol. , 2, 333–353, 1995) under the strong error model.

Availability: Freely available upon request.

Contact: skiena{at}cs.sunysb.edu


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[Abstract] [PDF]


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