Patent ID: 7809509

Claim:
A method for predicting a sequence of at least a first nucleic acid comprising the steps of: (a) identifying by a sequencing method a first plurality of subsequences from said first nucleic acid; (b) comparing by a computer program stored in a computer the first plurality of subsequences with at least a second nucleic acid sequence; (c) identifying by said computer program stored in a computer for each subsequence from said first plurality a matching subsequence within said second nucleic acid sequence, the matching subsequences occurring at a distance from each otherwithin said second nucleic acid sequence; (d) determining relative position of each of said matching subsequences within second nucleic acid sequence, said relative position of matching subsequences comprising a number indicating distance between said matching subsequences within second nucleic acid sequence; and (e) assembling, using a computer program stored in a computer, said first plurality of subsequences into a sequence assembly by simultaneously (i) maximizing overlap between said first plurality of subsequences; and (ii) minimizing the difference between the relative position of said first plurality of subsequences in the sequence assembly and the relative position of their corresponding said matching subsequences within second nucleic acid sequence; whereby the sequence assembly predicts the sequence of at least said first nucleic acid.