New constructive heuristics for DNA sequencing by hybridization

Authors:
Christian Blum;Mateu Yábar Vallès
Affiliations:
ALBCOM, Dept. Llenguatges i Sistemes Informàtics, Universitat Politècnica de Catalunya, Barcelona, Spain;ALBCOM, Dept. Llenguatges i Sistemes Informàtics, Universitat Politècnica de Catalunya, Barcelona, Spain
Venue:
WABI'06 Proceedings of the 6th international conference on Algorithms in Bioinformatics
Year:
2006

Citing 4
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DNA Sequencing--Tabu and Scatter Search Combined

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Probabilistic nucleotide assembling method for sequencing by hybridization

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Using an adaptive memory strategy to improve a multistart heuristic for sequencing by hybridization

WEA'05 Proceedings of the 4th international conference on Experimental and Efficient Algorithms

An ant colony optimization algorithm for DNA sequencing by hybridization

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Accurate Reconstruction for DNA Sequencing by Hybridization Based on a Constructive Heuristic

IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)

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Abstract

Deoxyribonucleic acid (DNA) sequencing is an important task in computational biology. In recent years the specific problem of DNA sequencing by hybridization has attracted quite a lot of interest in the optimization community. However, in contrast to the development of metaheuristics, the work on simple constructive heuristics hardly received any attention. This is despite the fact that well-working constructive heuristics are often an essential component of succesful metaheuristics. It is exactly this lack of constructive heuristics that motivated the work presented in this paper. The results of our best constructive heuristic are comparable to the results of the best available metaheuristics, while using less computational resources.