Patent ID: 8065091

Claim:
A method of engineering a given transcript of a given gene in a given organism in order to regulate expression of the given transcript, wherein the method is run on a system comprising one or more distinct components, each of the one or more distinct components being embodied on a tangible computer-readable recordable storage medium, the method comprising: identifying one or more regions of interest in a sequence of the given transcript, wherein identifying one or more regions of interest in a sequence of the given transcript is carried out by a component executing on a hardware processor; sub-selecting, within the one or more identified regions of interest, a motif, wherein sub-selecting a motif comprises identifying one or more identically conserved copies of the motif in intergenic and intronic regions of the genome of interest and identifying one or more additional copies in untranslated and amino acid coding regions of one or more genes in the genome of interest, wherein sub-selecting a motif further comprises using a pattern discovery technique with a pre-determined parameter of minimum size of discovered pattern and a pre-determined parameter of minimum required number of discovered copies before a pattern can be deemed as identified, and further wherein sub-selecting a motif is carried out by a component executing on a hardware processor; and using the one or more sub-selected regions to make one or more modifications to the sequence of the given transcript, wherein using the one or more sub-selected regions to make one or more modifications to the sequence of the given transcript is carried out by a component executing on a hardware processor.