Sequencing-by-hybridization at the information-theory bound: an optimal algorithm
RECOMB '00 Proceedings of the fourth annual international conference on Computational molecular biology
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
Computers and Intractability: A Guide to the Theory of NP-Completeness
Computers and Intractability: A Guide to the Theory of NP-Completeness
MFCS '94 Proceedings of the 19th International Symposium on Mathematical Foundations of Computer Science 1994
On the Complexity of Positional Sequencing by Hybridization
CPM '99 Proceedings of the 10th Annual Symposium on Combinatorial Pattern Matching
Sequencing by hybridization in few rounds
Journal of Computer and System Sciences
Optimal probing patterns for sequencing by hybridization
WABI'06 Proceedings of the 6th international conference on Algorithms in Bioinformatics
| Hi-index | 0.00 |
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.