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. A candidate nucleotide sequence having an essentially maximal
score is selected and one or more
low confidence intervals and one or more reliable intervals in the selected candidate nucleotide sequence are identified. For each
low confidence interval detected in the selected candidate nucleotide sequence, a
score is assigned to each of a plurality of candidate nucleotide sequences of the
low confidence region, where the score is based upon a probabilistic spectrum obtained by filtering from the PS signals the signals present in the reliable regions; and upon an interval of the reference nucleotide sequence H homologous with the low
confidence interval. A candidate nucleotide sequence having an essentially maximal score is then selected. A revised candidate sequence S′ is then obtained indicative of the sequence of the target polynucleotide molecule T by substituting the sequence of the low
confidence region in the candidate sequence S with the selected candidate sequence.