Spectrum Alignment: Efficient Resequencing by Hybridization
Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology
Restricting SBH Ambiguity via Restriction Enzymes
WABI '02 Proceedings of the Second International Workshop on Algorithms in Bioinformatics
Enhanced Sequence Reconstruction with DNA Microarray Application
COCOON '01 Proceedings of the 7th Annual International Conference on Computing and Combinatorics
On the Complexity of Positional Sequencing by Hybridization
CPM '99 Proceedings of the 10th Annual Symposium on Combinatorial Pattern Matching
Reconstructing strings from substrings in rounds
FOCS '95 Proceedings of the 36th Annual Symposium on Foundations of Computer Science
On spaced seeds for similarity search
Discrete Applied Mathematics
Designing seeds for similarity search in genomic DNA
Journal of Computer and System Sciences - Special issue on bioinformatics II
A unifying framework for seed sensitivity and its application to subset seeds
WABI'05 Proceedings of the 5th International conference on Algorithms in Bioinformatics
CIAA'07 Proceedings of the 12th international conference on Implementation and application of automata
Sequencing by hybridization in few rounds
Journal of Computer and System Sciences
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Sequencing by Hybridization (SBH) is a method for reconstructing a DNA sequence based on its k-mer content. This content, called the spectrum of the sequence, can be obtained from hybridization with a universal DNA chip. The main shortcoming of SBH is that it reliably reconstructs only sequences of length at most square root of the size of the chip. Frieze et al. [9] showed that by using gapped probes, SBH can reconstruct sequences with length that is linear in the size of the chip. In this work we investigate the optimal placement of the gaps in the probes, and give an algorithm for finding nearly optimal gap placement. Using our algorithm, we obtain a chip design which is more efficient than the chip of Frieze et al.