Patent ID: 6060248
Filing Date: 2000-05-09
Classification: C12Q

Abstract:
A method of identifying sites on a nucleic acid sequence having a desired melting free energy variability comprising:providing a nucleotide sequence;calculating a melting free energy of a plurality of windows centered on a base pair for a plurality of base pairs from the nucleotide sequence, wherein said plurality of windows are of a size between 2 and Y, wherein Y is an integer between 3 and 100;for each window size, constructing a melting free energy distribution along the sequence, normalizing the distribution to a standard scale;determining mean normalized melting free energy values for all windows for each base pair position; andproviding the deviation from the mean normalized melting free energy value of each base position for each window at the same base position; and selecting the sites with the largest deviation as the sites having the desired melting free energy variability.