Patent ID: 8014955

Claim:
A non-transient tangible computer readable medium containing computer readable instructions that when executed by one or more processors, cause the one or more processors to execute a method for designing a target-specific oligonucleotide sequence having an L-length in a polynucleotide population comprising polynucleotide targets, the method comprising: a) exhaustively parsing a polynucleotide target into overlapping polynucleotide sequences of N-length nucleotides to create an N-length nucleotides kernel set for each target; b) performing step a) reiteratively for each polynucleotide target that is a member of the polynucleotide population, until each polynucleotide target is associated with its own N-length nucleotide kernel set; c) removing N-length nucleotide kernels from the N-length nucleotide kernel sets which are present in more than one N-length nucleotide kernel set; d) choosing X-length nucleotide suffixes for each N-length nucleotide kernel, wherein the suffix consists of an X-length sequence of nucleotides that is upstream or downstream of the kernel, and optionally separated by a gap of nucleotides; e) ordering L-length nucleotides consecutively within each set of step d) by their nucleotide position within the target polynucleotide, wherein each L-length nucleotide comprises consecutive and overlapping kernels; f) 1) retaining an L-length oligonucleotide, if each of the X consecutive and overlapping N-length kernels are present after step e), wherein each of the X consecutive kernels comprise at least one nucleotide of the X-length suffix; and f) 2) rejecting an L-length oligonucleotide, if at least one of the X consecutive and overlapping N-length kernels is absent after steps e), wherein each of the X consecutive kernels comprise at least one nucleotide of the X-length suffix; g) performing steps f)1 and f)2 reiteratively, beginning with the X+1 N-length kernel when all X-length suffixes are present; or beginning with the kernel immediately following the absent suffix; and h) displaying the results of step (g) in a computer readable format to determine the identity of said target specific oligonucleotide sequence.