  A hypercomplex representation of DNA is proposed to facilitate comparison of
DNA sequences with fuzzy composition. Using hypercomplex number representation,
conventional sequence analysis method, such as, dot matrix analysis, dynamic
programming, and cross-correlation method are extended and improved to align
the DNA sequences with fuzzy composition. The hypercomplex dot matrix analysis
can provide more control over the degree of alignment desired. A new scoring
system has been proposed to accommodate the hypercomplex number representation
of DNA and integrated with dynamic programming alignment method. By using
hypercomplex cross-correlation, matching and mismatching alignment information
between two aligned DNA sequences are stored in the resultant real part and
imaginary parts, respectively. Mismatching alignment information is
particularly useful for refining consensus sequence-based motif scanning.
