US Patent 7343249 Vectorization of sequence alignment computation using distance matrix reshaping

A method for comparing data sequences includes accepting first and second data sequences of data elements. A distance matrix is computed. The matrix includes rows and columns of matrix elements, describing distances between the data elements of the first sequence and the data elements of the second data sequence. The distance matrix is reshaped by applying successive, incremental shifts to the rows or columns so as to produce a reshaped matrix. A best-score path through the reshaped matrix is calculated using vector operations, so as to quantify a similarity between the first and second data sequences.