Dealing with errors in interactive sequencing by hybridization.

V T Phan; S S Skiena

doi:10.1093/bioinformatics/17.10.862

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Dealing with errors in interactive sequencing by hybridization.

V T Phan·S S Skiena

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Abstract

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. AVAILABILTY: Freely available upon request. CONTACT: skiena@cs.sunysb.edu.

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Algorithms Computational Biology False Negative Reactions False Positive Reactions Models, Statistical Nucleic Acid Hybridization Oligonucleotide Probes Sequence Analysis, DNA Journal Article

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V T Phan, S S Skiena. 2001. Dealing with errors in interactive sequencing by hybridization.. https://doi.org/10.1093/bioinformatics%2F17.10.862

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