Patent ID: 6251588
Filing Date: 2001-06-26
Classification: G16B

Abstract:
A method for predicting the potential of an oligonucleotide to hybridze to a target nucleotide sequence, said method comprising:(a) identifying a predetermined number of unique oligonucleotides of at least 5 nucleotides in length within a nucleotide sequence of at least 30 nucleotides in length that is hybridizable with said target nucleotide sequence, said oligonucleotides being chosen to sample the entire length of said nucleotide sequence,(b) determining and evaluating for each of said oligonucleotides at least one parameter that is independently predictive of the ability of each of said oligonucleotides to hybridize to said target nucleotide sequence,(c) selecting a subset of oligonucleotides within said predetermined number of unique oligonucleotides based on an examination of said parameter and application of a rule that rejects some of said oligonucleotides of step (b),(d) identifying oligonucleotides in said selected subset, viewed according to order of position along said nucleotide sequence, that are clustered along a region of said nucleotide sequence, and,(e) selecting, from said oliaonucleotides identified in step (d), oligonucleotides of higher hybridization potential for said target nucleotide sequence wherein the larger the size of said clusters, the higher said hybridization potential.