Computational complexity of isothermic DNA sequencing by hybridization

Authors:
Jacek Blazewicz;Marta Kasprzak
Affiliations:
Institute of Computing Science, Poznan University of Technology, Poznan, Poland and Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland;Institute of Computing Science, Poznan University of Technology, Poznan, Poland and Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
Venue:
Discrete Applied Mathematics - Special issue: IV ALIO/EURO workshop on applied combinatorial optimization
Year:
2006

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Abstract

In the paper, the computational complexity of several variants of the problem of isothermic DNA sequencing by hybridization, is analyzed. The isothermic sequencing is a recent method, in which isothermic oligonucleotide libraries are used during the hybridization with an unknown DNA fragment. The variants of the isothermic DNA sequencing problem with errors in the hybridization data, negative ones or positive ones, are proved to be strongly NP-hard. On the other hand, the polynomial time algorithm for the ideal case with no errors is proposed.