Using fuzzy logic to confirm the integrity of a pattern recognition algorithm for long genomic sequences: the W-curve

The W-curve is a numerical mapping algorithm that provides tertiary information content of long and short genomic sequences. The most popular genomic pattern recognition algorithms depend on string matching of the primary information content of short genomic sequences. Herein, we describe a way to define the fuzzy properties of the W-curve. This approach improves a distance (dissimilarity) between two or more homologous long genomic sequences. Fourier analysis of W-curves delivers a smoother function for gap-stripped regions. Calculation of respective Fourier energies may improve the accuracy of the distance metric used to generate a phylogenetic tree of analyzed genomic sequences. This is especially the case for long genomic sequences that have been gap-stripped and aligned with the aid of previously published heuristic methods. These previous methods involved W-curve alignments used in concert with such programs as Clustal that use linear dynamic programming to align multiple gap-stripped W-curves.