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DNA sequencing by hybridization with additional information available

Formanowicz P.

Computational Methods in Science and Technology

2005

Vol. 11, nr 1

21-29

In classical DNA sequencing by hybridization it is assumed that the information obtained in the biochemical stage of the method is a set of the l-tuples composing the target sequence. It means that the information concerning the number of the repeated l-tuples is not available. Such an assumption was justified by the DNA chip technology constraints. However, nowadays some approximate information about l-tuple multiplicities can be obtained in the experiments, where DNA chips are used. It was a motivation for formulating combinatorial problems which arise when such additional information is taken into account. The goal of this paper is to formulate and classify these problems, what should establish a good starting point for further research concerning algorithmic methods solving DNA sequencing problems with multiplicity information. Moreover, the computational complexity of the new problems is determined, which in most cases is analogous to the complexity of their classical counterparts.