Abstract: A method for obtaining a candidate nucleotide sequence S indicative of a sequence of a target polynucleotide molecule that produces a hybridization signal I({right arrow over (x)}) upon incubation with a polynucleotide {right arrow over (x)} for each polynucleotide {right arrow over (x)} in a set E of polynucleotides. For each polynucleotide {right arrow over (x)} in the set E of polynucleotides, a probability P0({right arrow over (x)}) of the hybridization signal I({right arrow over (x)}) when the sequence {right arrow over (x)} is not complementary to a subsequence of T and a probability P1({right arrow over (x)}) of the hybridization signal when the sequence {right arrow over (x)} is complementary to a subsequence of T are obtained; so as to obtain a probabilistic spectrum (PS) of T. A score is then assigned to each of a plurality of candidate nucleotide sequences that is being based upon the probabilistic spectrum and upon a reference nucleotide sequence H.