Hypercomplex cross-correlation of DNA sequences
Shu, Jian Jun
Date of Issue2010
School of Mechanical and Aerospace Engineering
A hypercomplex representation of DNA is proposed to facilitate comparing DNA sequences with fuzzy composition. With the hypercomplex number representation, the conventional sequence analysis method, such as, dot matrix analysis, dynamic programming, and cross-correlation method have been extended and improved to align 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, the match and mismatch alignment information between two aligned DNA sequences are separately stored in the resultant real part and imaginary parts respectively. The mismatch alignment information is very useful to refine consensus sequence based motif scanning.
Journal of biological systems
© 2010 World Scientific Publishing Company. This is the author created version of a work that has been peer reviewed and accepted for publication by Journal of Biological Systems, World Scientific Publishing Company. It incorporates referee’s comments but changes resulting from the publishing process, such as copyediting, structural formatting, may not be reflected in this document. The published version is available at: [DOI: http://dx.doi.org/10.1142/s0218339010003470].