Patent ID: 7962316

Claim:
A method for selecting from a plurality of different siRNAs one or more siRNAs for silencing a target gene in an organism, each different siRNA in said plurality of different siRNAs targeting a different target sequence in a transcript of said target gene, said method comprising (a) calculating a score for a corresponding targeted sequence motif in said transcript, for each said different siRNA in said plurality of different siRNAs, wherein said score is calculated using a position-specific score matrix (PSSM), wherein each said sequence motif is a nucleotide sequence of L nucleotides, L being an integer, and wherein said PSSM is {log(e ij /p ij )}, where e ij is the weight of nucleotide i at position j, p ij is the weight of nucleotide i at position j in a random sequence, and i=G or C, A, U(T), j=1, . . . L, wherein each of said targeted sequence motifs comprises at least a portion of the target sequence of the corresponding siRNA and/or a second sequence in a sequence region flanking said target sequence; (b) ranking said plurality of different siRNAs according to said scores; and (c) selecting one or more siRNAs from said ranked siRNAs, wherein at least one of steps (a), (b) or (c) is performed by a suitably programmed computer.