PROFILE SEARCHING IN NUCLEIC ACID SEQUENCES USING THE FAST FOURIER TRANSFORMATION

摘要

The present invention provides methods for detecting known blocks offunctionally aligned protein sequences in atest nucleic acid sequence in a test nucleic acid sequence, based on the totalnumber of base matches for the variety of possible tags.This method reverse-translates common protein alignments to nucleic acidprofiles, using recently tabulated codon frequencies. Themethod then performs a search for the known nucleic acid profiles by obtainingthe correlation of different based between a testnucleic acid sequence and the known nucleic acid profile. This is efficientlyachieved in the frequency domain by use of a FastFourier Transform.