Patent ID: 6957148

Claim:
A method for assigning parameters of antisense effectiveness to 64 next-nearest-neighbor nucleotide triplets from measurements of the antisense effectiveness of at least 64 nucleotide sequences, wherein the sequences are considered to be closed sequences without end effects comprising: (a) constructing a matrix X having N rows and M columns, wherein said matrix X has one row for each of a minimum of N=64 nucleotide symbolic sequences and one column for each of the possible M=64 types of next-nearest-neighbor nucleotide triplets for symbolic sequences containing the common four nucleotides, A, U, G, and C, wherein the numbers in the matrix columns are the numbers of each type of next-nearest-neighbor nucleotide triplet in the sequence in the given row; (b) constructing a matrix Y with N rows and 1 column, wherein the numbers in the rows are measured values corresponding to the biological antisense effectiveness of the N symbolic sequences; (c) dividing the rows of matrices X and Y by the respective errors in the measured values; (d) constructing a matrix P having M rows and 1 column, wherein the elements in the rows are variables representing the 64 parameters of antisense effectiveness assigned to the next-nearest-neighbor nucleotide triplets; (e) solving equation X multiplied by P equals Y via the singular value decomposition method, wherein said equation is solved for P; (f) assigning P values as parameters of antisense effectiveness to next-nearest neighbor nucleotide triplets; and (g) displaying antisense effectiveness parameters.