Abstract
The expected number of n-base long sequences consistent with a given SBH spectrum grows exponentially with n, which severely limits the potential range of applicability of SBH even in an error-free setting. Restriction enzymes (RE) recognize specific patterns and cut the DNA molecule at all locations of that pattern. The output of a restriction assay is the set of lengths of the resulting fragments. By augmenting the SBH spectrum with the target string’s RE spectrum, we can eliminate much of the ambiguity of SBH. In this paper, we build on [20] to enhance the resolving power of restriction enzymes. We give a hardness result for the SBH+RE problem, and supply improved heuristics for the existing backtracking algorithm. We prove a lower bound on the number restriction enzymes required for unique reconstruction, and show experimental results that are not far from this bound.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
G. Andrews. The Theory of Partitions. Addison-Wesley, Reading, Mass., 1976.
R. Arratia, D. Martin, G. Reinert, and M. Waterman. Poisson process approximation for sequence repeats, and sequencing by hybridization. J. Computational Biology, 3:425–463, 1996.
W. Bains and G. Smith. A novel method for nucleic acid sequence determination. J. Theor. Biol., 135:303–307, 1988.
A. Ben-Dor, I. Pe’er, R. Shamir, and R. Sharan. On the complexity of positional sequencing by hybridization. Lecture Notes in Computer Science, 1645:88–98, 1999.
A. Chetverin and F. Kramer. Oligonucleotide arrays: New concepts and possibilities. Bio/Technology, 12:1093–1099, 1994.
N.G. de Bruijn. A combinatorial problem. Proc. Kon. Ned. Akad. Wetensch, 49:758–764, 1946.
R. Dramanac and R. Crkvenjakov. DNA sequencing by hybridization. Yugoslav Patent Application 570, 1987.
S. Fodor, J. Read, M. Pirrung, L. Stryer, A. Lu, and D. Solas. Light-directed, spatially addressable parallel chemical synthesis. Science, 251:767–773, 1991.
A. Frieze and B. Halldorsson. Optimal sequencing by hybridization in rounds. In Proc. Fifth Conf. on Computational Molecular Biology (RECOMB-01), pages 141–148, 2001.
M. R. Garey and D. S. Johnson. Computers and Intractability: A Guide to the theory of NP-completeness. W. H. Freeman, San Francisco, 1979.
Y. Lysov, V. Florentiev, A. Khorlin, K. Khrapko, V. Shik, and A. Mirzabekov. Determination of the nucleotide sequence of dna using hybridization to oligonucleotides. Dokl. Acad. Sci. USSR, 303:1508–1511, 1988.
P. Pevzner, Y. Lysov, K. Khrapko, A. Belyavski, V. Florentiev, and A. Mizabelkov. Improved chips for sequencing by hybridization. J. Biomolecular Structure & Dynamics, 9:399–410, 1991.
P. A. Pevzner and R. J. Lipshutz. Towards DNA sequencing chips. 19th Int. Conf. Mathematical Foundations of Computer Science, 841:143–158, 1994.
P.A. Pevzner. l-tuple DNA sequencing: Computer analysis.J. Biomolecular Structure and Dynamics, 7:63–73, 1989.
V. Phan and S. Skiena. Dealing with errors in interactive sequencing by hybridization. Bioinformatics, 17:862–870, 2001.
F. P. Preparata and E. Upfal. Sequencing-by-hybridization at the informationtheory bound: An optimal algorithm. In Proc. Fourth Conf. Computational Molecular Biology (RECOMB-00), pages 245–253, 2000.
R. Roberts. Rebase: the restriction enzyme database. http://rebase.neb.com, 2001.
R. Shamir and D. Tsur. Large scale sequencing by hybridization. In Proc. Fifth International Conf. on Computational Molecular Biology (RECOMB-01), pages 269–277, 2001.
S. Skiena and G. Sundaram. Reconstructing strings from substrings. J. Computational Biology, 2:333–353, 1995.
S. Snir, E. Yeger-Lotem, B. Chor, and Z. Yakhini. Using restriction enzymes to improve sequencing by hybridization. Technical Report CS-2002-14, Department of Computer Science,The Technion, Haifa, Israel, 2002.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2002 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Skiena, S., Snir, S. (2002). Restricting SBH Ambiguity via Restriction Enzymes. In: GuigĂł, R., Gusfield, D. (eds) Algorithms in Bioinformatics. WABI 2002. Lecture Notes in Computer Science, vol 2452. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-45784-4_30
Download citation
DOI: https://doi.org/10.1007/3-540-45784-4_30
Published:
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-44211-0
Online ISBN: 978-3-540-45784-8
eBook Packages: Springer Book Archive