TN curve: A novel 3D graphical representation of DNA sequence based on trinucleotides and its applications

被引：66
作者：
Yu, Jia-Feng [1 ,2 ]
Sun, Xiao [1 ]
Wang, Ji-Hua [2 ]
机构：
[1] Southeast Univ, Sch Biol Sci & Med Engn, State Key Lab Bioelect, Nanjing 210096, Peoples R China
[2] Dezhou Univ, Dept Phys, Key Lab Biophys, Shandong Univ, Dezhou 253023, Peoples R China
来源：
JOURNAL OF THEORETICAL BIOLOGY | 2009年 / 261卷 / 03期
基金：
中国国家自然科学基金;
关键词：
Numerical descriptor; Similarity/dissimilarity analysis; Projection; Coding sequence; CODON USAGE; NUMERICAL CHARACTERIZATION; SIMILARITY ANALYSIS; CELLULAR-AUTOMATA; QSAR MODEL; RATE LAWS; STEADY; RULES; SIMILARITY/DISSIMILARITY; PROTEINS;
D O I：
10.1016/j.jtbi.2009.08.005
中图分类号：
Q [生物科学];
学科分类号：
07 ; 0710 ; 09 ;
摘要：
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. (C) 2009 Elsevier Ltd. All rights reserved.
引用
收藏
页码：459 / 468
页数：10
相关论文
共 65 条
  • [1] ALTHAUS IW, 1993, J BIOL CHEM, V268, P14875
  • [2] ALTHAUS IW, 1993, J BIOL CHEM, V268, P6119
  • [3] KINETIC-STUDIES WITH THE NONNUCLEOSIDE HIV-1 REVERSE-TRANSCRIPTASE INHIBITOR-U-88204E
    ALTHAUS, IW
    CHOU, JJ
    GONZALES, AJ
    DEIBEL, MR
    CHOU, KC
    KEZDY, FJ
    ROMERO, DL
    PALMER, JR
    THOMAS, RC
    ARISTOFF, PA
    TARPLEY, WG
    REUSSER, F
    [J]. BIOCHEMISTRY, 1993, 32 (26) : 6548 - 6554
  • [4] Kinetic plasticity and the determination of product ratios for kinetic schemes leading to multiple products without rate laws - New methods based on directed graphs
    Andraos, John
    [J]. CANADIAN JOURNAL OF CHEMISTRY, 2008, 86 (04) : 342 - 357
  • [5] A group of 3D graphical representation of DNA sequences based on dual nucleotides
    Cao, Zhi
    Liao, Bo
    Li, Renfa
    [J]. INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, 2008, 108 (09) : 1485 - 1490
  • [6] Chen WY, 2008, MATCH-COMMUN MATH CO, V60, P291
  • [7] Novel 4D numerical representation of DNA sequences
    Chi, R
    Ding, KQ
    [J]. CHEMICAL PHYSICS LETTERS, 2005, 407 (1-3) : 63 - 67
  • [8] GRAPHICAL RULES FOR ENZYME-CATALYZED RATE LAWS
    CHOU, KC
    FORSEN, S
    [J]. BIOCHEMICAL JOURNAL, 1980, 187 (03) : 829 - 835
  • [9] 2 NEW SCHEMATIC RULES FOR RATE LAWS OF ENZYME-CATALYZED REACTIONS
    CHOU, KC
    [J]. JOURNAL OF THEORETICAL BIOLOGY, 1981, 89 (04) : 581 - 592
  • [10] GRAPHICAL RULES FOR NON-STEADY STATE ENZYME-KINETICS
    CHOU, KC
    LIU, WM
    [J]. JOURNAL OF THEORETICAL BIOLOGY, 1981, 91 (04) : 637 - 654
1234567