Descriptors for DNA Sequences Based on Joint Diagonalization of Their Feature Matrices from Dinucleotide Physicochemical Properties

Numerical characterizations of DNA sequence can facilitate analysis of similar sequences. To visualize and compare different DNA sequences in less space, a novel descriptors extraction approach was proposed for numerical characterizations and similarity analysis of sequences. Initially, a transformation method was introduced to represent each DNA sequence with dinucleotide physicochemical property matrix. Then, based on the approximate joint diagonalization theory, an eigenvalue vector was extracted from each DNA sequence, which could be considered as descriptor of the DNA sequence. Moreover, similarity analyses were performed by calculating the pair-wise distances among the obtained eigenvalue vectors. The results show that the proposed approach can capture more sequence information, and can jointly analyze the information contained in all involved multiple sequences, rather than separately, whose effectiveness was demonstrated intuitively by constructing a dendrogram for the 15 beta-globin gene sequences.