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Volumn 41, Issue 3, 2008, Pages 217-222

2-D graphical representation of protein sequences and its application to coronavirus phylogeny

Author keywords

ALE index; Coronavirus; Graphical representation; Phylogeny; Protein

Indexed keywords

CORONAVIRUS;

EID: 42049104155     PISSN: 12258687     EISSN: 02191024     Source Type: Journal    
DOI: 10.5483/bmbrep.2008.41.3.217     Document Type: Article
Times cited : (38)

References (49)
  • 3
    • 0022592245 scopus 로고
    • A simple way to look at DNA
    • Gates, M. A. (1986) A simple way to look at DNA. J. Theor. Biol. 119, 319-328.
    • (1986) J. Theor. Biol , vol.119 , pp. 319-328
    • Gates, M.A.1
  • 4
    • 0000678497 scopus 로고    scopus 로고
    • A novel 2-D graphical representation of DNA sequences of low degeneracy
    • Guo, X. F., Randić, M. and Basak, S. C. (2001) A novel 2-D graphical representation of DNA sequences of low degeneracy. Chem. Phys. Lett. 350, 106-112.
    • (2001) Chem. Phys. Lett , vol.350 , pp. 106-112
    • Guo, X.F.1    Randić, M.2    Basak, S.C.3
  • 5
    • 0020659327 scopus 로고
    • H curves, a novel method of representation of nucleotide series especially suited for long DNA sequences
    • Hamori, E. and Ruskin, J. (1983) H curves, a novel method of representation of nucleotide series especially suited for long DNA sequences. J. Biol. Chem. 258, 1318.
    • (1983) J. Biol. Chem , vol.258 , pp. 1318
    • Hamori, E.1    Ruskin, J.2
  • 6
    • 0025340372 scopus 로고
    • Chaos game representation of gene structure
    • Jeffrey, H. I. (1990) Chaos game representation of gene structure. Nucleic Acid Res. 18, 2163-2170.
    • (1990) Nucleic Acid Res , vol.18 , pp. 2163-2170
    • Jeffrey, H.I.1
  • 7
    • 0028889673 scopus 로고
    • Random walk and gap plots of DNA sequences
    • Leong, P. M. and Morgenthaler, S. (1995) Random walk and gap plots of DNA sequences. Comput. Applic. Biosci. 12, 503-511.
    • (1995) Comput. Applic. Biosci , vol.12 , pp. 503-511
    • Leong, P.M.1    Morgenthaler, S.2
  • 8
    • 1542514776 scopus 로고    scopus 로고
    • On a 3-D representation of DNA primary sequences
    • Li, C. and Wang, J. (2004) On a 3-D representation of DNA primary sequences. Comb. Chem. High T. Scr. 7, 23-27.
    • (2004) Comb. Chem. High T. Scr , vol.7 , pp. 23-27
    • Li, C.1    Wang, J.2
  • 9
    • 33745615095 scopus 로고    scopus 로고
    • Directed graphs of DNA sequences and their numerical characterization
    • Li, C., Tang, N. N. and Wang, J. (2006) Directed graphs of DNA sequences and their numerical characterization. J. Theor. Biol. 241, 173-177.
    • (2006) J. Theor. Biol , vol.241 , pp. 173-177
    • Li, C.1    Tang, N.N.2    Wang, J.3
  • 10
    • 33744953166 scopus 로고    scopus 로고
    • 2-D Graphical representation for characteristic sequences of DNA and its application
    • Li, C. and Hu, J. (2006) 2-D Graphical representation for characteristic sequences of DNA and its application. J. Biochem. Mol. Biol. 39, 292-296.
    • (2006) J. Biochem. Mol. Biol , vol.39 , pp. 292-296
    • Li, C.1    Hu, J.2
  • 11
    • 0000347441 scopus 로고
    • A new graphical representation and analysis of DNA sequence structure: I. Methodology and application to globin genes
    • Nandy, A. (1994) A new graphical representation and analysis of DNA sequence structure: I. Methodology and application to globin genes. Curr. Sci. 66, 309-313.
    • (1994) Curr. Sci , vol.66 , pp. 309-313
    • Nandy, A.1
  • 12
    • 0013068398 scopus 로고
    • Graphical representation of long DNA sequences
    • Nandy, A. (1994) Graphical representation of long DNA sequences. Curr. Sci. 66, 821.
    • (1994) Curr. Sci , vol.66 , pp. 821
    • Nandy, A.1
  • 13
    • 33749518282 scopus 로고    scopus 로고
    • Mathematical descriptors of DNA sequences: Development and applications
    • Nandy, A., Harle, M. and Basak, S. C. (2006) Mathematical descriptors of DNA sequences: development and applications. ARKIVOC 9, 211-238.
    • (2006) ARKIVOC , vol.9 , pp. 211-238
    • Nandy, A.1    Harle, M.2    Basak, S.C.3
  • 14
    • 0034266159 scopus 로고    scopus 로고
    • On 3-D graphical representation of DNA primary sequence and their numerical characterization
    • Randić, M., Vracko, M., Nandy, A. and Basak, S. C. (2000) On 3-D graphical representation of DNA primary sequence and their numerical characterization. J. Chem. Inf. Comput. Sci. 40, 1235-1244.
    • (2000) J. Chem. Inf. Comput. Sci , vol.40 , pp. 1235-1244
    • Randić, M.1    Vracko, M.2    Nandy, A.3    Basak, S.C.4
  • 15
    • 0035324934 scopus 로고    scopus 로고
    • On the Characterization of DNA primary sequences by triplet of nucleic acid bases
    • Randić, M., Guo, X. F. and Basak S. C. (2001) On the Characterization of DNA primary sequences by triplet of nucleic acid bases. J. Chem. Inf. Comptu. Sci. 41, 619-626.
    • (2001) J. Chem. Inf. Comptu. Sci , vol.41 , pp. 619-626
    • Randić, M.1    Guo, X.F.2    Basak, S.C.3
  • 16
    • 0037363676 scopus 로고    scopus 로고
    • On a four-dimensional representation of DNA primary sequences
    • Randić, M. and Balaban, A. T. (2003) On a four-dimensional representation of DNA primary sequences. J. Chem. Inf. Comptu. Sci. 43, 532-539.
    • (2003) J. Chem. Inf. Comptu. Sci , vol.43 , pp. 532-539
    • Randić, M.1    Balaban, A.T.2
  • 17
    • 0037435485 scopus 로고    scopus 로고
    • Novel 2-D graphical representation of DNA sequences and their numerical characterization
    • Randić, M., Vracko, M., Lers, N. and Plavsić, D. (2003) Novel 2-D graphical representation of DNA sequences and their numerical characterization. Chem. Phys. Lett. 368, 1-6.
    • (2003) Chem. Phys. Lett , vol.368 , pp. 1-6
    • Randić, M.1    Vracko, M.2    Lers, N.3    Plavsić, D.4
  • 18
    • 0037470662 scopus 로고    scopus 로고
    • Analysis of similarity/dissimilarity of DNA sequences based on novel 2-D graphical representation
    • Randić, M., Vracko, M., Lers, N. and Plavsić, D. (2003) Analysis of similarity/dissimilarity of DNA sequences based on novel 2-D graphical representation. Chem. Phys. Lett. 371, 202-207.
    • (2003) Chem. Phys. Lett , vol.371 , pp. 202-207
    • Randić, M.1    Vracko, M.2    Lers, N.3    Plavsić, D.4
  • 19
  • 20
    • 1442336331 scopus 로고    scopus 로고
    • Graphical representations of DNA as 2-D map
    • Randić, M. (2004) Graphical representations of DNA as 2-D map. Chem. Phys. Lett. 386, 468-471.
    • (2004) Chem. Phys. Lett , vol.386 , pp. 468-471
    • Randić, M.1
  • 21
    • 2442500682 scopus 로고    scopus 로고
    • Highly compact 2-D graphical representation of DNA sequences
    • Randić, M. and Zupan, J. (2004) Highly compact 2-D graphical representation of DNA sequences. SAR QSAR Environ. Res. 15, 191-205.
    • (2004) SAR QSAR Environ. Res , vol.15 , pp. 191-205
    • Randić, M.1    Zupan, J.2
  • 22
    • 0031953432 scopus 로고    scopus 로고
    • A novel technique of graphical representation and analysis of DNA sequences-A review
    • Roy, A., Raychaudhury, C. and Nandy, A. (1998) A novel technique of graphical representation and analysis of DNA sequences-A review. J. Biosci. 23, 55-71.
    • (1998) J. Biosci , vol.23 , pp. 55-71
    • Roy, A.1    Raychaudhury, C.2    Nandy, A.3
  • 23
    • 0037413312 scopus 로고    scopus 로고
    • DB-Curve: A novel 2D method of DNA sequence visualization and representation
    • Wu, Y. H., Liew, A. W., Yan, H. and Yang, M. (2003) DB-Curve: a novel 2D method of DNA sequence visualization and representation. Chem. Phys. Lett. 367, 170-176.
    • (2003) Chem. Phys. Lett , vol.367 , pp. 170-176
    • Wu, Y.H.1    Liew, A.W.2    Yan, H.3    Yang, M.4
  • 24
    • 0027995001 scopus 로고
    • Z curves, an intuitive tool for visualizing and analyzing DNA sequences
    • Zhang, R. and Zhang, C. T. (1994) Z curves, an intuitive tool for visualizing and analyzing DNA sequences. J. Biomol. Struc. Dyn. 11, 767-782.
    • (1994) J. Biomol. Struc. Dyn , vol.11 , pp. 767-782
    • Zhang, R.1    Zhang, C.T.2
  • 25
    • 2442509138 scopus 로고    scopus 로고
    • 2-D Graphical representation of proteins based on virtual genetic code
    • Randić, M. (2004) 2-D Graphical representation of proteins based on virtual genetic code. SAR QSAR Environ. Res. 15, 147-157.
    • (2004) SAR QSAR Environ. Res , vol.15 , pp. 147-157
    • Randić, M.1
  • 26
    • 7444235858 scopus 로고    scopus 로고
    • Unique graphical representation of protein sequences based on nucleotide triplet codons
    • Randić, M., Zupan, J. and Balaban, A. T. (2004) Unique graphical representation of protein sequences based on nucleotide triplet codons. Chem. Phys. Lett. 397, 247-252.
    • (2004) Chem. Phys. Lett , vol.397 , pp. 247-252
    • Randić, M.1    Zupan, J.2    Balaban, A.T.3
  • 28
    • 32344433839 scopus 로고    scopus 로고
    • Novel 2-D graphical representation of proteins
    • Randić, M., Butina, D. and Zupan, J. (2006) Novel 2-D graphical representation of proteins. Chem. Phys. Lett. 419, 528-532.
    • (2006) Chem. Phys. Lett , vol.419 , pp. 528-532
    • Randić, M.1    Butina, D.2    Zupan, J.3
  • 29
    • 34250857482 scopus 로고    scopus 로고
    • On representation of proteins by star-like graphs
    • Randić, M., Zupan, J. and Vikić-Topić, D. (2007) On representation of proteins by star-like graphs. J. Mol. Graph. Model. 26, 290-305.
    • (2007) J. Mol. Graph. Model , vol.26 , pp. 290-305
    • Randić, M.1    Zupan, J.2    Vikić-Topić, D.3
  • 30
    • 25444531712 scopus 로고    scopus 로고
    • Severe acute respiratory syndrome coronavirus-like virus in Chinese horseshoe bats
    • Lau, S. K. P., Wo, P. C. Y. and Li, K. S. M., et al. (2005) Severe acute respiratory syndrome coronavirus-like virus in Chinese horseshoe bats. PNAS 102, 14040-14045.
    • (2005) PNAS , vol.102 , pp. 14040-14045
    • Lau, S.K.P.1    Wo, P.C.Y.2    Li, K.S.M.3
  • 31
    • 0038823524 scopus 로고    scopus 로고
    • The genome sequence of the sars-associated coronavirus
    • Marra, M. A., Jones, S. J. M. and Astell, C. R., et al. (2003) The genome sequence of the sars-associated coronavirus. Science 300, 1399.
    • (2003) Science , vol.300 , pp. 1399
    • Marra, M.A.1    Jones, S.J.M.2    Astell, C.R.3
  • 33
    • 0037561920 scopus 로고    scopus 로고
    • Characterization of a novel coronavirus associated with severe acute respiratory syndrome
    • Rota, P. A., Oberste, M. S. and Monroe, S. S., et al. (2003) Characterization of a novel coronavirus associated with severe acute respiratory syndrome. Science 300, 1394.
    • (2003) Science , vol.300 , pp. 1394
    • Rota, P.A.1    Oberste, M.S.2    Monroe, S.S.3
  • 34
    • 34250335677 scopus 로고    scopus 로고
    • The Molecular Biology of SARS Coronavirus
    • Satija, N. and Lal, S. (2007) The Molecular Biology of SARS Coronavirus. Ann. N.Y. Acad. Sci. 1102, 26-38.
    • (2007) Ann. N.Y. Acad. Sci , vol.1102 , pp. 26-38
    • Satija, N.1    Lal, S.2
  • 35
    • 1242268097 scopus 로고    scopus 로고
    • Molecular phylogeny of coronaviruses including human SARS-CoV
    • Gao, L., Qi, J., Wei, H. B., Sun, Y. G. and Hao, B. L. (2003) Molecular phylogeny of coronaviruses including human SARS-CoV. Chin. Sci. Bull. 48, 1170-1174.
    • (2003) Chin. Sci. Bull , vol.48 , pp. 1170-1174
    • Gao, L.1    Qi, J.2    Wei, H.B.3    Sun, Y.G.4    Hao, B.L.5
  • 36
    • 3242695128 scopus 로고    scopus 로고
    • Severe acute respiratory syndrome coronavirus phylogeny: Toward consensus
    • Gorbalenya, A. E., Snijder, E. J. and Spaan, W. J. M. (2004) Severe acute respiratory syndrome coronavirus phylogeny: toward consensus. J. Virol. 78, 7863-7866.
    • (2004) J. Virol , vol.78 , pp. 7863-7866
    • Gorbalenya, A.E.1    Snijder, E.J.2    Spaan, W.J.M.3
  • 37
    • 0038076030 scopus 로고    scopus 로고
    • A novel coronavirus associated with severe acute respiratory syndrome
    • Ksiazek, T. G., Zaki, S. R. and Urbani, C., et al. (2003) A novel coronavirus associated with severe acute respiratory syndrome. N. Engl. J. Med. 348, 1953-1966.
    • (2003) N. Engl. J. Med , vol.348 , pp. 1953-1966
    • Ksiazek, T.G.1    Zaki, S.R.2    Urbani, C.3
  • 39
    • 0042164218 scopus 로고    scopus 로고
    • Unique and conserved features of genome and proteome of SARS-coronavirus, an early split-off from the coronavirus group 2 lineage
    • Snijder, E. J., Bredenbeek, P. J. and Dobbe, J. C., et al. (2003) Unique and conserved features of genome and proteome of SARS-coronavirus, an early split-off from the coronavirus group 2 lineage. J. Mol. Biol. 331, 991-1004.
    • (2003) J. Mol. Biol , vol.331 , pp. 991-1004
    • Snijder, E.J.1    Bredenbeek, P.J.2    Dobbe, J.C.3
  • 41
    • 12144286761 scopus 로고    scopus 로고
    • Molecular evolution of the SARS coronavirus during the course of the SARS epidemic in China
    • Chinese SARS Molecular Epidemiology Consortium
    • Chinese SARS Molecular Epidemiology Consortium. (2004) Molecular evolution of the SARS coronavirus during the course of the SARS epidemic in China. Science 303, 1666-1669.
    • (2004) Science , vol.303 , pp. 1666-1669
  • 42
    • 42049095591 scopus 로고    scopus 로고
    • A review of studies on animal reservoirs of the SARS coronavirus
    • in press
    • Shi, Z. and Hu, Z. (2007) A review of studies on animal reservoirs of the SARS coronavirus. Virus Res. in press.
    • (2007) Virus Res
    • Shi, Z.1    Hu, Z.2
  • 43
    • 20044382817 scopus 로고    scopus 로고
    • Cross-host evolution of severe acute respiratory syndrome coronavirus in palm civet and human
    • Song, H. D., Tu, C. C. and Zhang, G. W., et al. (2005) Cross-host evolution of severe acute respiratory syndrome coronavirus in palm civet and human. PNAS 102, 2430-2435.
    • (2005) PNAS , vol.102 , pp. 2430-2435
    • Song, H.D.1    Tu, C.C.2    Zhang, G.W.3
  • 44
    • 0032726679 scopus 로고    scopus 로고
    • A computational approach to simplifying the protein folding problem
    • Wang, J. and Wang, W. (1999) A computational approach to simplifying the protein folding problem. Nat. Struct. Biol. 6, 1033 -1038.
    • (1999) Nat. Struct. Biol , vol.6 , pp. 1033-1038
    • Wang, J.1    Wang, W.2
  • 45
    • 0034195180 scopus 로고    scopus 로고
    • Modeling study on the validity of a possibly simplified representation of proteins
    • Wang, J. and Wang, W. (2000) Modeling study on the validity of a possibly simplified representation of proteins. Phys. Rev. E. 61, 6981-6986.
    • (2000) Phys. Rev. E , vol.61 , pp. 6981-6986
    • Wang, J.1    Wang, W.2
  • 47
    • 33845362256 scopus 로고    scopus 로고
    • Characterization of Complex Biological Systems by Matrix Invariants
    • Jaklic, G., Pisanski, T. and Randić, M. (2006) Characterization of Complex Biological Systems by Matrix Invariants. J. Comput. Biol. 13, 1558-1564.
    • (2006) J. Comput. Biol , vol.13 , pp. 1558-1564
    • Jaklic, G.1    Pisanski, T.2    Randić, M.3
  • 48
    • 13844306521 scopus 로고    scopus 로고
    • New Invariant of DNA Sequences
    • Li, C. and Wang, J. (2005) New Invariant of DNA Sequences. J. Chem. Inf. Model. 45, 115-120.
    • (2005) J. Chem. Inf. Model , vol.45 , pp. 115-120
    • Li, C.1    Wang, J.2
  • 49
    • 0036985129 scopus 로고    scopus 로고
    • Novel matrix invariants for characterization of changes of proteomics maps
    • Randić, M., Zupan, J., Novic, M., Gute, B. D. and Basak, S. C. (2002) Novel matrix invariants for characterization of changes of proteomics maps. SAR QSAR Environ. Res. 13, 689-703.
    • (2002) SAR QSAR Environ. Res , vol.13 , pp. 689-703
    • Randić, M.1    Zupan, J.2    Novic, M.3    Gute, B.D.4    Basak, S.C.5


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