Analysis of Similarity/Dissimilarity of DNA Sequences Based on Nonoverlapping Triplets of Nucleotide Bases

We consider a 6-D representation of triplets of nucleotide bases of DNA sequences. Based on this representation, we outline an approach by constructing a 3-component vector whose components are the normalized leading eigenvalues of the L/L matrices associated with the triplets derived from DNA sequences. The examination of similarities/dissimilarities among the coding sequences of the first exon of beta-globin gene of different species illustrates the utility of the approach.

[1]  E. Hamori,et al.  H curves, a novel method of representation of nucleotide series especially suited for long DNA sequences. , 1983, The Journal of biological chemistry.

[2]  A. Nandy.  GRAPHICAL ANALYSIS OF DNA SEQUENCE STRUCTURE : III. INDICATIONS OF EVOLUTIONARY DISTINCTIONS AND CHARACTERISTICS OF INTRONS AND EXONS , 1996 .

[3]  Dejan Plavšić,et al.  Novel 2-D graphical representation of DNA sequences and their numerical characterization , 2003 .

[4]  Milan Randic.  Condensed Representation of DNA Primary Sequences , 2000, J. Chem. Inf. Comput. Sci..

[5]  A. Nandy.  A new graphical representation and analysis of DNA sequence structure. I: Methodology and application to globin genes , 1994 .

[6]  A. Nandy,et al.  GRAPHICAL ANALYSIS OF DNA SEQUENCE STRUCTURE. II: RELATIVE ABUNDANCES OF NUCLEOTIDES IN DNAS, GENE EVOLUTION AND DUPLICATION , 1995 .

[7]  R Zhang,et al.  Z curves, an intutive tool for visualizing and analyzing the DNA sequences. , 1994, Journal of biomolecular structure & dynamics.

[8]  Dejan Plavšić,et al.  DNA invariants based on nonoverlapping triplets of nucleotide bases , 2003 .

[9]  Bo Liao,et al.  New 3D graphical representation of DNA sequences and their numerical characterization , 2003 .

[10]  Milan Randic,et al.  On the Characterization of DNA Primary Sequences by Triplet of Nucleic Acid Bases , 2001, J. Chem. Inf. Comput. Sci..

[11]  Dejan Plavšić,et al.  Analysis of similarity/dissimilarity of DNA sequences based on novel 2-D graphical representation , 2003 .

[12]  Bo Liao,et al.  Analysis of similarity/dissimilarity of DNA sequences based on 3-D graphical representation , 2004 .