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

Abstract: 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 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. [Copyright &y& Elsevier]