Novel graphical representation of genome sequence and its applications in similarity analysis

In order to compare different genome sequences, an alignment-free method has been proposed. Considering the essential property of sequence is sequentiality, we define a compound transformation which transforms a genome sequence into a sparse 16 by L − 1 matrix M based on 16 kinds of 2-mer (dinucleotides). Furthermore, we found the transformation above-mentioned is an order-preserving transformation (OPT). Based on the theory of matrix analysis, we derive a 16-dimensional vector to characterize a genome sequence via singular value decomposition (SVD) of M. Finally, we analyze the similarities among multiple sequences from 20 eutherian species. The experiment results show that our approach performs well in the field of sequence analysis.