A 3D graphical representation of protein sequences based on the Gray code

被引：32
作者：
He, Ping-an [1 ]
Li, Dan [1 ]
Zhang, Yanping [2 ,3 ]
Wang, Xin [4 ]
Yao, Yuhua [5 ]
机构：
[1] Zhejiang Sci Tech Univ, Coll Sci, Hangzhou 310018, Peoples R China
[2] Nankai Univ, Coll Math Sci, Tianjin 300071, Peoples R China
[3] Nankai Univ, LPMC, Tianjin 300071, Peoples R China
[4] Dalian Naval Acad, Dalian 116018, Peoples R China
[5] Zhejiang Sci Tech Univ, Coll Life Sci, Hangzhou 310018, Peoples R China
来源：
JOURNAL OF THEORETICAL BIOLOGY | 2012年 / 304卷
关键词：
Binary code; CGR; Mathematical descriptors; Correlation and significance analysis; PHYSICOCHEMICAL PROPERTIES; SIMILARITY/DISSIMILARITY; PREDICTION;
D O I：
10.1016/j.jtbi.2012.03.023
中图分类号：
Q [生物科学];
学科分类号：
07 ; 0710 ; 09 ;
摘要：
Based on the order of 6-bit binary Gray code, a cyclic order of 20 amino acids is introduced. A novel 3D graphical representation of protein sequences is proposed according to the CGR of DNA sequences. Furthermore, the mathematical descriptor is suggested to characterize the graphical representation curve. The efficiency of our approach can be illustrated by performing the comparison of similarities/dissimilarities among sequences of the ND5 proteins of nine different species. With the correlation and significance analysis, the comparisons of both our results and results of other graphical representation with the ClustalW's results can show the utility of our approach. (c) 2012 Elsevier Ltd. All rights reserved.
引用
收藏
页码：81 / 87
页数：7
相关论文
共 32 条
[1]   On graphical and numerical representation of protein sequences [J].
Bai, FL ;
Wang, TM .
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 2006, 23 (05) :537-545
[2]   Prediction of Enzyme Classes from 3D Structure: A General Model and Examples of Experimental-Theoretic Scoring of Peptide Mass Fingerprints of Leishmania Proteins [J].
Concu, Riccardo ;
Dea-Ayuela, Maria A. ;
Perez-Montoto, Lazaro G. ;
Bolas-Fernandez, Francisco ;
Prado-Prado, Francisco J. ;
Podda, Gianni ;
Uriarte, Eugenio ;
Ubeira, Florencio M. ;
Gonzalez-Diaz, Humberto .
JOURNAL OF PROTEOME RESEARCH, 2009, 8 (09) :4372-4382
[3]   3D graphical representation of protein sequences and their statistical characterization [J].
el Maaty, Moheb I. Abo ;
Abo-Elkhier, Mervat M. ;
Abd Elwahaab, Marwa A. .
PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS, 2010, 389 (21) :4668-4676
[4]   Characterization of protein primary sequences based on partial ordering [J].
Feng, Jie ;
Wang, Tian-Ming .
JOURNAL OF THEORETICAL BIOLOGY, 2008, 254 (04) :752-755
[5]   Generalized lattice graphs for 2D-visualization of biological information [J].
Gonzalez-Diaz, H. ;
Perez-Montoto, L. G. ;
Duardo-Sanchez, A. ;
Paniagua, E. ;
Vazquez-Prieto, S. ;
Vilas, R. ;
Dea-Ayuela, M. A. ;
Bolas-Fernandez, F. ;
Munteanu, C. R. ;
Dorado, J. ;
Costas, J. ;
Ubeira, F. M. .
JOURNAL OF THEORETICAL BIOLOGY, 2009, 261 (01) :136-147
[6]   A new graphical representation of similarity/dissimilarity studies of protein sequences [J].
He, P. .
SAR AND QSAR IN ENVIRONMENTAL RESEARCH, 2010, 21 (5-6) :571-580
[7]  
He PA, 2011, MATCH-COMMUN MATH CO, V65, P445
[8]   The Graphical Representation of Protein Sequences Based on the Physicochemical Properties and Its Applications [J].
He, Ping-An ;
Zhang, Yan-Ping ;
Yao, Yu-Hua ;
Tang, Yi-Fa ;
Nan, Xu-Ying .
JOURNAL OF COMPUTATIONAL CHEMISTRY, 2010, 31 (11) :2136-2142
[9]   CHAOS GAME REPRESENTATION OF GENE STRUCTURE [J].
JEFFREY, HJ .
NUCLEIC ACIDS RESEARCH, 1990, 18 (08) :2163-2170
[10]   Clustal W and clustal X version 2.0 [J].
Larkin, M. A. ;
Blackshields, G. ;
Brown, N. P. ;
Chenna, R. ;
McGettigan, P. A. ;
McWilliam, H. ;
Valentin, F. ;
Wallace, I. M. ;
Wilm, A. ;
Lopez, R. ;
Thompson, J. D. ;
Gibson, T. J. ;
Higgins, D. G. .
BIOINFORMATICS, 2007, 23 (21) :2947-2948
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