Patent ID: 6785613
Filing Date: 2004-08-31
Classification: C07K,C12N,C12Q,G01N,G16B

Abstract:
A computer-implemented method for selecting a target site within a polynucleotide for targeting by a zinc finger protein, comprising:providing a polynucleotide sequence; selecting a potential target site within the polynucleotide sequence; the potential target site comprising contiguous first, second and third triplets of bases at first, second and third positions in the potential target site; determining a plurality of subscores by applying a correspondence regime between triplets and triplet position in a sequence of three contiguous triplets, wherein each triplet has first, second and third corresponding positions, and each combination of triplet and triplet position has a particular subscore, the subscore being a value indicating the desirability of the triplet occupying the triplet position, and the correspondence regime being a matrix of subscores for combinations of triplets and triplet positions; calculating a score for the potential target site by combining subscores for the first, second, and third triplets; repeating the selecting, determining and calculating steps at least once on a further potential target site comprising first, second and third triplets at first, second and third positions of the further potential target site to determine a further score; providing output of at least one potential target site with its score.