Similarity/ dissimilarity analysis of flowering plant DNA sequences

Abstract

1 Department of Mathematics, Jinan University, Guangzhou, 510632, China \u00a0 (Received November 06 2019, accepted December 28 2019) The multiple sequence alignment (MSA) is a usual tool in DNA sequence comparison. However, this method meets a hard challenge for a large number of long DNA sequences. To remedy this problem, we propose \u00a0a \u00a0new \u00a0way \u00a0for \u00a0DNA \u00a0sequence \u00a0comparison \u00a0based \u00a0on \u00a0a \u00a0novel \u00a0DNA \u00a0map. \u00a0The \u00a0method \u00a0is \u00a0that, \u00a0by assigning a dinucleotide to a number, we construct a new graphical representation of DNA sequences based on horizontal \u00a0lines. \u00a0We \u00a0further \u00a0utilize \u00a0the \u00a0maximal \u00a0eigenvalue \u00a0of \u00a0a \u00a0related \u00a0matrix \u00a0to \u00a0derive \u00a0a \u00a0mathematical descriptor \u00a0for \u00a0a \u00a0DNA \u00a0sequence. \u00a0We \u00a0also \u00a0perform \u00a0the \u00a0similarity/dissimilarity \u00a0analysis \u00a0among \u00a0the \u00a0coding sequences of ribulose bisphosphate carboxylase small chain gene and large chain gene of flowering plants. The results indicate that this method can be reliable in the comparison of the flowering plant DNA sequences.