Patent ID: 8594951

Claim:
A computer implemented method of aligning nucleic acid sequence information for at least one of a sample nucleic acid template against a candidate reference nucleic acid sequence, the method comprising: flowing a series of nucleotide flows to a plurality of defined spaces resulting in one or more nucleotide incorporate events detecting a plurality of signals from the defined spaces corresponding the one or more nucleotide incorporation events; identifying a candidate nucleic acid sequence based upon the plurality of signals and respective nucleobases associated with respective flows of the series of nucleotide flows; mapping the candidate nucleic acid sequence to a reference genome to determine a reference nucleic acid sequence; forming, for one or more nucleobases of the series of nucleotide flows, a matrix of cells comprising a first dimension corresponding to the nucleobases of the reference nucleic acid sequence and a second dimension comprising homopolymer lengths from 0 to n for homopolymeric incorporations of nucleobases associated with respective nucleotide flows; calculating a value for selected cells of the matrix reflecting the overlap of the nucleobase of the nucleotide flow with nucleobases of the reference nucleic acid sequence using a local sequence alignment method; weighting the values of the matrix based upon the respective signal of the nucleobase of the nucleotide flow; traversing the matrix to determine an aligned nucleic acid sequence; and outputting the aligned nucleic acid sequence.