Patent ID: 8050869
Filing Date: 2011-11-01
Classification: G16B

Abstract:
1. A method of computing the number of matches between a test nucleic acid sequence and a profile for a set of functionally aligned nucleic acid sequences comprising the steps of A) constructing a first indicator function for the profile, said indicator function corresponding to a first base, said indicator function continuous between 0 and 1 for a value at a given position as a function of the percentage presence of the first base at a particular position, B) constructing a second indicator function for the test nucleic acid sequence, said indicator function corresponding to the first base, C) computing in a computer the Fourier transform of each of the indicator functions, D) complex conjugating the Fourier transform of the second indicator function, E) multiplying the Fourier transform of the first indicator function and the complex conjugated Fourier transform of the second indicator function to obtain a Fourier transform for adenine base matches, F) repeating steps A-E above for a second base, a third base, and a fourth base, G) summing the Fourier transforms of the number of matches for each base, respectively, to obtain the total Fourier transform, H) computing the inverse Fourier transform of the total Fourier transform to obtain a complex series, said complex series comprising a real part, and I) taking the real part of the series to determine the total number of base matches for the variety of possible lags of the profile relative to the test sequence, and J) displaying said base matches, wherein said nucleic acid sequence profile is a DNA profile, wherein said method further comprises the step of reverse-translating a protein profile for a set of protein sequences to obtain said DNA profile, said reverse translation being performed using codon-usage tables, said reverse translation step occurring before step (A).