Optimal sequencing by hybridization in rounds
RECOMB '01 Proceedings of the fifth annual international conference on Computational biology
Large scale sequencing by hybridization
RECOMB '01 Proceedings of the fifth annual international conference on Computational biology
Spectrum Alignment: Efficient Resequencing by Hybridization
Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology
MFCS '94 Proceedings of the 19th International Symposium on Mathematical Foundations of Computer Science 1994
Computational complexity of isothermic DNA sequencing by hybridization
Discrete Applied Mathematics - Special issue: IV ALIO/EURO workshop on applied combinatorial optimization
Sequencing by hybridization with errors: handling longer sequences
Theoretical Computer Science
DNA Sequencing by Hybridization via Genetic Search
Operations Research
Computational complexity of isothermic DNA sequencing by hybridization
Discrete Applied Mathematics - Special issue: IV ALIO/EURO workshop on applied combinatorial optimization
Tight bounds for string reconstruction using substring queries
APPROX'05/RANDOM'05 Proceedings of the 8th international workshop on Approximation, Randomization and Combinatorial Optimization Problems, and Proceedings of the 9th international conference on Randamization and Computation: algorithms and techniques
Tabu search algorithm for DNA sequencing by hybridization with isothermic libraries
Computational Biology and Chemistry
Hi-index | 0.00 |
Sequencing by hybridization (SBH) is a DNA sequencing technique, in which the sequence is reconstructed using its k-mer content. This content, which is called the spectrum of the sequence, is obtained by hybridization to a universal DNA array. Standard universal arrays contain all k-mers for some fixed k, typically 8 to 10. Currently, in spite of its promise and elegance, SBH is not competitive with standard gel-based sequencing methods. This is due to two main reasons: lack of tools to handle realistic levels of hybridization errors, and an inherent limitation on the length of uniquely reconstructible sequence by standard universal arrays.In this paper we deal with both problems. We introduce a simple polynomial reconstruction algorithm which can be applied to spectra from standard arrays and has provable performance in the presence of both false negative and false positive errors. We also propose a novel design of chips containing universal bases, that differs from the one proposed by Preparata et al. We give a simple algorithm that uses spectra from such chips to reconstruct with high probability random sequences of length lower only by a squared log factor compared to the information theoretic bound. Our algorithm is very robust to errors, and has a provable performance even if there are both false negative and false positive errors. Simulations indicate that its sensitivity to errors is also very small in practice.