메뉴 건너뛰기




Volumn 241, Issue 2, 2013, Pages 217-224

C-curve: A novel 3D graphical representation of DNA sequence based on codons

Author keywords

3D codon curve; DNA sequence; P Matrix; S Matrix; Similarities dissimilarities

Indexed keywords

3D CODON CURVE; 3D GRAPHICAL REPRESENTATION; DNA MUTATION; NUMERICAL CHARACTERIZATION; P-MATRIX; QUANTITATIVE COMPARISON; S-MATRIX; SIMILARITIES/DISSIMILARITIES;

EID: 84872145606     PISSN: 00255564     EISSN: 18793134     Source Type: Journal    
DOI: 10.1016/j.mbs.2012.11.009     Document Type: Article
Times cited : (50)

References (36)
  • 1
    • 0020659327 scopus 로고
    • H curves, a novel method of representation of nucleotide series especially suited for long DNA sequences
    • Hamori E., Ruskin J. H curves, a novel method of representation of nucleotide series especially suited for long DNA sequences. J. Biol. Chem. 1983, 258:1318.
    • (1983) J. Biol. Chem. , vol.258 , pp. 1318
    • Hamori, E.1    Ruskin, J.2
  • 3
    • 0000347441 scopus 로고
    • A new graphical representation and analysis of DNA sequence structure I. Methodology and application to globin genes
    • Nandy A. A new graphical representation and analysis of DNA sequence structure I. Methodology and application to globin genes. Curr. Sci. 1994, 66:309.
    • (1994) Curr. Sci. , vol.66 , pp. 309
    • Nandy, A.1
  • 5
    • 0037460960 scopus 로고    scopus 로고
    • The Z-curve databases: a graphic representation of genome sequence
    • Zhang C.T., Zhang R., Ou H.Y. The Z-curve databases: a graphic representation of genome sequence. Bioinformatics 2003, 19:593.
    • (2003) Bioinformatics , vol.19 , pp. 593
    • Zhang, C.T.1    Zhang, R.2    Ou, H.Y.3
  • 6
    • 0027995001 scopus 로고
    • Z curve, an intuitive tool for visualizing and analyzing the DNA sequences
    • Zhang R., Zhang C.T. Z curve, an intuitive tool for visualizing and analyzing the DNA sequences. J. Biomol. Struct. Dyn. 1994, 11:767.
    • (1994) J. Biomol. Struct. Dyn. , vol.11 , pp. 767
    • Zhang, R.1    Zhang, C.T.2
  • 7
    • 33749518282 scopus 로고    scopus 로고
    • Mathematical descriptors of DNA sequences
    • Nandy A., Harle M., Basak S.C. Mathematical descriptors of DNA sequences. ARKIVOC 2006, 9:211.
    • (2006) ARKIVOC , vol.9 , pp. 211
    • Nandy, A.1    Harle, M.2    Basak, S.C.3
  • 8
    • 3142704623 scopus 로고    scopus 로고
    • New 2D graphical representation of DNA sequences
    • Liao B., Wang T.M. New 2D graphical representation of DNA sequences. J. Comput. Chem. 2004, 25:1364.
    • (2004) J. Comput. Chem. , vol.25 , pp. 1364
    • Liao, B.1    Wang, T.M.2
  • 9
    • 33845372678 scopus 로고    scopus 로고
    • 3D graphical representation of DNA sequence without degeneracy and its applications in constructing phylogenic tree
    • Liao B., Zhu W., Liu Y. 3D graphical representation of DNA sequence without degeneracy and its applications in constructing phylogenic tree. MATCH Commun. Math. Comput. Chem. 2006, 56:209.
    • (2006) MATCH Commun. Math. Comput. Chem. , vol.56 , pp. 209
    • Liao, B.1    Zhu, W.2    Liu, Y.3
  • 10
    • 10644258114 scopus 로고    scopus 로고
    • A 2D graphical representation of DNA sequence
    • Liao B. A 2D graphical representation of DNA sequence. Chem. Phys. Lett. 2005, 401:196.
    • (2005) Chem. Phys. Lett. , vol.401 , pp. 196
    • Liao, B.1
  • 11
    • 0034266159 scopus 로고    scopus 로고
    • On 3-D graphical representation of DNA primary sequences and their numerical characterization
    • Randić M., Vraćko M., Nandy A., Basak S.C. On 3-D graphical representation of DNA primary sequences and their numerical characterization. J. Chem. Inf. Comput. Sci. 2000, 40:1235-1244.
    • (2000) J. Chem. Inf. Comput. Sci. , vol.40 , pp. 1235-1244
    • Randić, M.1    Vraćko, M.2    Nandy, A.3    Basak, S.C.4
  • 12
    • 77951135004 scopus 로고    scopus 로고
    • Analysis of similarities/dissimilarities of DNA sequences based on a novel graphical representation
    • Yu J.F., Wang J.H., Sun X. Analysis of similarities/dissimilarities of DNA sequences based on a novel graphical representation. MATCH Commun. Math. Comput. Chem. 2010, 63:493.
    • (2010) MATCH Commun. Math. Comput. Chem. , vol.63 , pp. 493
    • Yu, J.F.1    Wang, J.H.2    Sun, X.3
  • 13
    • 0037363676 scopus 로고    scopus 로고
    • On a four-dimensional representation of DNA primary sequences
    • Randić M., Balaban A.T. On a four-dimensional representation of DNA primary sequences. J. Chem. Inf. Comput. Sci. 2003, 43:532-539.
    • (2003) J. Chem. Inf. Comput. Sci. , vol.43 , pp. 532-539
    • Randić, M.1    Balaban, A.T.2
  • 14
    • 0020659327 scopus 로고
    • A novel method of representation of nucleotide series especially suited for long DNA sequences
    • Hamori E., Ruskin J., Curves H. A novel method of representation of nucleotide series especially suited for long DNA sequences. J. Biol. Chem. 1983, 258:1318.
    • (1983) J. Biol. Chem. , vol.258 , pp. 1318
    • Hamori, E.1    Ruskin, J.2    Curves, H.3
  • 15
    • 1542636606 scopus 로고    scopus 로고
    • Graphical analysis of DNA sequence structure: III. Indications of evolutionary distinctions and characteristics of introns and exons
    • Nandy A. Graphical analysis of DNA sequence structure: III. Indications of evolutionary distinctions and characteristics of introns and exons. Curr. Sci. 1996, 70:661.
    • (1996) Curr. Sci. , vol.70 , pp. 661
    • Nandy, A.1
  • 16
    • 0037435480 scopus 로고    scopus 로고
    • On the uniqueness of quantitative DNA difference descriptors in 2D graphical representation models
    • Nandy A. On the uniqueness of quantitative DNA difference descriptors in 2D graphical representation models. Chem. Phys. Lett. 2003, 368:102.
    • (2003) Chem. Phys. Lett. , vol.368 , pp. 102
    • Nandy, A.1
  • 17
    • 0037450561 scopus 로고    scopus 로고
    • Numerical characterization of DNA sequences in a 2-D graphical representation scheme of low degeneracy
    • Guo X., Nandy X. Numerical characterization of DNA sequences in a 2-D graphical representation scheme of low degeneracy. Chem. Phys. Lett. 2003, 369:361.
    • (2003) Chem. Phys. Lett. , vol.369 , pp. 361
    • Guo, X.1    Nandy, X.2
  • 18
  • 19
    • 84872148154 scopus 로고    scopus 로고
    • A Novel Composition Coding Method of DNA Sequence and Its Application
    • Wu R., Hu Q., Li R., Yue G. A Novel Composition Coding Method of DNA Sequence and Its Application. MATCH Commun. Math. Comput. Chem. 2012, 67:269.
    • (2012) MATCH Commun. Math. Comput. Chem. , vol.67 , pp. 269
    • Wu, R.1    Hu, Q.2    Li, R.3    Yue, G.4
  • 20
    • 80155214043 scopus 로고    scopus 로고
    • A novel approach for the classical ramsey number problem on DNA-based supercomputing
    • Zhou X., Li K., Goodman M., Sallam A. A novel approach for the classical ramsey number problem on DNA-based supercomputing. MATCH Commun. Math. Comput. Chem. 2011, 66:347.
    • (2011) MATCH Commun. Math. Comput. Chem. , vol.66 , pp. 347
    • Zhou, X.1    Li, K.2    Goodman, M.3    Sallam, A.4
  • 22
    • 33745615095 scopus 로고    scopus 로고
    • Directed graphs of DNA sequences and their numerical characterization
    • Li C., Tang N., Wang J. Directed graphs of DNA sequences and their numerical characterization. J. Theor. Biol. 2006, 241:173.
    • (2006) J. Theor. Biol. , vol.241 , pp. 173
    • Li, C.1    Tang, N.2    Wang, J.3
  • 23
    • 33747383589 scopus 로고    scopus 로고
    • Invariants of DNA sequences based on 2DD-curves
    • Zhang Y., Chen W. Invariants of DNA sequences based on 2DD-curves. J. Theor. Biol. 2006, 242:382.
    • (2006) J. Theor. Biol. , vol.242 , pp. 382
    • Zhang, Y.1    Chen, W.2
  • 24
    • 77955477421 scopus 로고    scopus 로고
    • New method for comparing DNA primary sequences based on a discrimination measure
    • Feng J., Hu Y., Wan P., Zhang A., Zhao W. New method for comparing DNA primary sequences based on a discrimination measure. J. Theor. Biol. 2010, 266:703.
    • (2010) J. Theor. Biol. , vol.266 , pp. 703
    • Feng, J.1    Hu, Y.2    Wan, P.3    Zhang, A.4    Zhao, W.5
  • 25
    • 33750835926 scopus 로고    scopus 로고
    • PNN-curve: a new 2D graphical representation of DNA sequences and its application
    • Liu X.Q., Dai Q., Xiu Z., Wang T. PNN-curve: a new 2D graphical representation of DNA sequences and its application. J. Theor. Biol. 2006, 243:55.
    • (2006) J. Theor. Biol. , vol.243 , pp. 55
    • Liu, X.Q.1    Dai, Q.2    Xiu, Z.3    Wang, T.4
  • 26
    • 84859636830 scopus 로고    scopus 로고
    • A 3D graphical representation of protein sequences based on the Gray code
    • He P., Li D., Zhang Y., Wang X., Yao Y. A 3D graphical representation of protein sequences based on the Gray code. J. Theor. Biol. 2012, 304:81-87.
    • (2012) J. Theor. Biol. , vol.304 , pp. 81-87
    • He, P.1    Li, D.2    Zhang, Y.3    Wang, X.4    Yao, Y.5
  • 27
    • 70350066201 scopus 로고    scopus 로고
    • TN curve: a novel 3D graphical representation of DNA sequence based on trinucleotides and its applications
    • Yu J.F., Sun X., Wang J.H. TN curve: a novel 3D graphical representation of DNA sequence based on trinucleotides and its applications. J. Theor. Biol. 2009, 261:459.
    • (2009) J. Theor. Biol. , vol.261 , pp. 459
    • Yu, J.F.1    Sun, X.2    Wang, J.H.3
  • 28
    • 36249019849 scopus 로고    scopus 로고
    • New 3D graphical representation of DNA sequence based on dual nucleotides
    • Qi X.Q., Wen J., Qi Z.H. New 3D graphical representation of DNA sequence based on dual nucleotides. J. Theor. Biol. 2007, 249:681.
    • (2007) J. Theor. Biol. , vol.249 , pp. 681
    • Qi, X.Q.1    Wen, J.2    Qi, Z.H.3
  • 29
    • 77958544124 scopus 로고    scopus 로고
    • Three 3D graphical representations of DNA primary sequences based on the classifications of DNA bases and their applications
    • Xie G., Mo Z. Three 3D graphical representations of DNA primary sequences based on the classifications of DNA bases and their applications. J. Theor. Biol. 2011, 269:123.
    • (2011) J. Theor. Biol. , vol.269 , pp. 123
    • Xie, G.1    Mo, Z.2
  • 30
    • 84872134670 scopus 로고    scopus 로고
    • A novel graphical and numerical representation for analyzing DNA sequences based on codons
    • Jafarzadeh N., Iranmanesh A. A novel graphical and numerical representation for analyzing DNA sequences based on codons. MATCH Commun. Math. Comput. Chem. 2012, 68:611.
    • (2012) MATCH Commun. Math. Comput. Chem. , vol.68 , pp. 611
    • Jafarzadeh, N.1    Iranmanesh, A.2
  • 31
    • 34548743514 scopus 로고    scopus 로고
    • Calculation of folding energies of single-strand nucleic acid sequences: conceptual issues
    • Forsdyke D.R. Calculation of folding energies of single-strand nucleic acid sequences: conceptual issues. J. Theor. Biol. 2007, 248:745.
    • (2007) J. Theor. Biol. , vol.248 , pp. 745
    • Forsdyke, D.R.1
  • 32
    • 46249100442 scopus 로고    scopus 로고
    • Computational discovery of cis-regulatory modules in Drosophila without prior knowledge of motifs
    • Ivan A., Halfon M.S., Sinha S. Computational discovery of cis-regulatory modules in Drosophila without prior knowledge of motifs. Genome Biol. 2008, 9:1.
    • (2008) Genome Biol. , vol.9 , pp. 1
    • Ivan, A.1    Halfon, M.S.2    Sinha, S.3
  • 34
    • 0037342499 scopus 로고    scopus 로고
    • Alignment-freesequencecomparison-a review
    • Vinga S., Almeida J. Alignment-freesequencecomparison-a review. Bioinformatics 2003, 19:513.
    • (2003) Bioinformatics , vol.19 , pp. 513
    • Vinga, S.1    Almeida, J.2
  • 36
    • 0036708519 scopus 로고    scopus 로고
    • Characteristic sequences for DNA primary sequence
    • He P., Wang J. Characteristic sequences for DNA primary sequence. J. Chem. Inf. Comput. Sci. 2002, 42:1080.
    • (2002) J. Chem. Inf. Comput. Sci. , vol.42 , pp. 1080
    • He, P.1    Wang, J.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.