TN curve: a novel 3D graphical representation of DNA sequence based on trinucleotides and its applications.
In this paper, a novel 3D graphical representation of DNA sequence based on trinucleotides is proposed. This representation allows direct inspection of composition as well as distribution of trinucleotides in DNA sequence for the first time and avoids loss of information, from which one can obtain more information. Based on this novel model, six numerical descriptors of DNA sequence are deduced without complicated calculations, and the applications in similarities/dissimilarities analysis of coding sequences and conserved genes discrimination illustrate their utilities. In addition, two simple methods for similarities/dissimilarities analysis of coding sequences among different species are exploited by using two vectors composed of 64 and six components, respectively, which can provide convenient sequence alignment tools for both computational scientists and molecular biologists.
Yu
Jia-Feng
JF
State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, PR China. bat3024@126.com
Sun
Xiao
X
Wang
Ji-Hua
JH
D000818:Animals; D001483:Base Sequence; D019295:Computational Biology / Q000379:methods; D006657:Histones / Q000235:genetics; D006801:Humans; D009690:Nucleic Acid Conformation; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA / Q000379:methods*; D013045:Species Specificity; D018911:Trinucleotide Repeats / Q000235:genetics*; D055544:beta-Globins / Q000235:genetics
D006657:Histones; D055544:beta-Globins
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