Patent ID: 7016788

Claim:
A method for comparing nucleic acids, said method comprising: (a) providing a first sample comprising a first population of first nucleic acids having different nucleotide sequences, and a second sample comprising a second population of second nucleic acids having different nucleotide sequences, wherein the nucleotide sequences of said second population are known; (b) probing said first sample with one or more recognition means, each recognition means recognizing a target nucleotide subsequence or a set of target nucleotide subsequences, wherein if said first sample is probed with two or more recognition means, each recognition means recognizes a different target nucleotide subsequence or a different set of target nucleotide subsequences; (c) generating one or more output signals from said first sample probed by said recognition means, each output signal comprising a representation of (i) the distance between occurrences of target nucleotide subsequences in said first nucleic acid, and (ii) the identities of said target nucleotide subsequences in said first nucleic acid or the identities of said sets of target nucleotide subsequences among which are included the target nucleotide subsequences in said first nucleic acid; and (d) comparing each representation provided by said first sample with said second population by generating (i) statistical score which states the probability that one or more output signals from said first sample indicates that one or more nucleotide sequences of said first sample are either present or absent in said second sample; and (ii) a statistical score of a false-negative rate or a false-positive rate, wherein said false-negative rate is a representation of the probability that said output from said first nucleic acid or said second nucleic acid is not generated given that said first or second nucleic acid is present, and said false-positive rate being a representation of the probability that said output from said first nucleic acid or said second nucleic acid is generated given that said first or second nucleic acid is not present.