메뉴 건너뛰기




Volumn 406, Issue , 2016, Pages 105-115

Protein sequence analysis by incorporating modified chaos game and physicochemical properties into Chou's general pseudo amino acid composition

Author keywords

Codon; Hydropathy index; Isoelectric point; Protein vector; Sequences analysis

Indexed keywords

AMINO ACID; CODON; HEMOGLOBIN BETA CHAIN; TRANSCRIPTION FACTOR;

EID: 84978712182     PISSN: 00225193     EISSN: 10958541     Source Type: Journal    
DOI: 10.1016/j.jtbi.2016.06.034     Document Type: Article
Times cited : (17)

References (59)
  • 2
    • 84875576158 scopus 로고    scopus 로고
    • Propy: a tool to generate various modes of Chou's PseAAC
    • Cao, D.S., Xu, Q.S., Liang, Y.Z., Propy: a tool to generate various modes of Chou's PseAAC. Bioinformatics 29 (2013), 960–962.
    • (2013) Bioinformatics , vol.29 , pp. 960-962
    • Cao, D.S.1    Xu, Q.S.2    Liang, Y.Z.3
  • 3
    • 84978780902 scopus 로고    scopus 로고
    • Phylogenetic analysis of protein sequences based on distribution of length about common substring
    • Chang, G., Wang, T., Phylogenetic analysis of protein sequences based on distribution of length about common substring. J. Comput. Bio. 13 (2011), 336–350.
    • (2011) J. Comput. Bio. , vol.13 , pp. 336-350
    • Chang, G.1    Wang, T.2
  • 4
    • 0027324791 scopus 로고
    • A joint prediction of the folding types of 1490 human proteins from their genetic codons
    • Chou, J.J., Zhang, C.T., A joint prediction of the folding types of 1490 human proteins from their genetic codons. J. Theor. Biol. 161 (1993), 251–262.
    • (1993) J. Theor. Biol. , vol.161 , pp. 251-262
    • Chou, J.J.1    Zhang, C.T.2
  • 5
    • 0024971003 scopus 로고
    • Graphic rules in steady and non-steady enzyme kinetics
    • Chou, K.C., Graphic rules in steady and non-steady enzyme kinetics. J. Biol. Chem. 264 (1989), 12074–12079.
    • (1989) J. Biol. Chem. , vol.264 , pp. 12074-12079
    • Chou, K.C.1
  • 6
    • 0025021607 scopus 로고
    • Review: applications of graph theory to enzyme kinetics and protein folding kinetics. steady and non-steady state systems
    • Chou, K.C., Review: applications of graph theory to enzyme kinetics and protein folding kinetics. steady and non-steady state systems. Biophys. Chem. 35 (1990), 1–24.
    • (1990) Biophys. Chem. , vol.35 , pp. 1-24
    • Chou, K.C.1
  • 7
    • 0026599046 scopus 로고
    • Energy-optimized structure of antifreeze protein and its binding mechanism
    • Chou, K.C., Energy-optimized structure of antifreeze protein and its binding mechanism. J. Mol. Biol. 233 (1992), 509–517.
    • (1992) J. Mol. Biol. , vol.233 , pp. 509-517
    • Chou, K.C.1
  • 8
    • 0035874091 scopus 로고    scopus 로고
    • Prediction of protein structural classes and subcellular locations
    • (Erratum: 2001, vol. 44, p. 60)
    • Chou, K.C., 2001. Prediction of protein structural classes and subcellular locations. Proteins: Struct. Funct. Genet. 43, 246–255 (Erratum: 2001, vol. 44, p. 60).
    • (2001) Proteins: Struct. Funct. Genet. , vol.43 , pp. 246-255
    • Chou, K.C.1
  • 9
    • 77952868004 scopus 로고    scopus 로고
    • Graphic rule for drug metabolism systems
    • Chou, K.C., Graphic rule for drug metabolism systems. Curr. Drug Metab. 11 (2010), 369–378.
    • (2010) Curr. Drug Metab. , vol.11 , pp. 369-378
    • Chou, K.C.1
  • 10
    • 79951518208 scopus 로고    scopus 로고
    • Some remarks on protein attribute prediction and pseudo amino acid composition (50th anniversary year review)
    • Chou, K.C., Some remarks on protein attribute prediction and pseudo amino acid composition (50th anniversary year review). J. Theor. Biol. 273 (2011), 236–247.
    • (2011) J. Theor. Biol. , vol.273 , pp. 236-247
    • Chou, K.C.1
  • 11
    • 54149091987 scopus 로고    scopus 로고
    • Comparison study on k-word statistical measures for protein: from sequence to sequence space
    • Dai, Q., Wang, T.M., Comparison study on k-word statistical measures for protein: from sequence to sequence space. BMC Bioinforma. 9 (2008), 1–19.
    • (2008) BMC Bioinforma. , vol.9 , pp. 1-19
    • Dai, Q.1    Wang, T.M.2
  • 13
    • 84859932176 scopus 로고    scopus 로고
    • PseAAC-Builder: a cross-platform stand-alone program for generating various special Chou's pseudo-amino acid compositions
    • Du, P., Wang, X., Xu, C., Gao, Y., PseAAC-Builder: a cross-platform stand-alone program for generating various special Chou's pseudo-amino acid compositions. Anal. Biochem. 425 (2012), 117–119.
    • (2012) Anal. Biochem. , vol.425 , pp. 117-119
    • Du, P.1    Wang, X.2    Xu, C.3    Gao, Y.4
  • 14
    • 84895429516 scopus 로고    scopus 로고
    • PseAAC-General: fast building various modes of general form of Chou's pseudo-amino acid composition for large-scale protein datasets
    • Du, P., Gu, S., Jiao, Y., PseAAC-General: fast building various modes of general form of Chou's pseudo-amino acid composition for large-scale protein datasets. Int. J. Mol. Sci. 15 (2014), 3495–3506.
    • (2014) Int. J. Mol. Sci. , vol.15 , pp. 3495-3506
    • Du, P.1    Gu, S.2    Jiao, Y.3
  • 15
    • 0032203376 scopus 로고    scopus 로고
    • Comparison of strings belonging to the same family
    • Elloumi, M., Comparison of strings belonging to the same family. Inf. Sci. 111 (1998), 49–63.
    • (1998) Inf. Sci. , vol.111 , pp. 49-63
    • Elloumi, M.1
  • 16
    • 0035057075 scopus 로고    scopus 로고
    • Molecular evolution of transferrin: evidence for positive selection in salmonids
    • Ford, M.J., Molecular evolution of transferrin: evidence for positive selection in salmonids. Mol. Biol. Evol. 18 (2001), 639–647.
    • (2001) Mol. Biol. Evol. , vol.18 , pp. 639-647
    • Ford, M.J.1
  • 17
    • 0019021450 scopus 로고
    • Graphical rules for enzyme-catalyzed rate laws
    • Forsen, S., Graphical rules for enzyme-catalyzed rate laws. Biochem. J. 187 (1980), 829–835.
    • (1980) Biochem. J. , vol.187 , pp. 829-835
    • Forsen, S.1
  • 19
    • 0020484488 scopus 로고
    • An improved algorithm for matching biological sequences
    • Gotoh, O., An improved algorithm for matching biological sequences. J. Mol. Biol. 162 (1982), 705–708.
    • (1982) J. Mol. Biol. , vol.162 , pp. 705-708
    • Gotoh, O.1
  • 20
    • 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. 258 (1983), 1318–1327.
    • (1983) J. Biol. Chem. , vol.258 , pp. 1318-1327
    • Hamori, E.1    Ruskin, J.2
  • 22
    • 0028505328 scopus 로고
    • Biological evaluation of d2, an algorithm for high-performance sequence comparison
    • Hide, W., Burke, J., Davison, D.B., Biological evaluation of d2, an algorithm for high-performance sequence comparison. J. Comput. Biol. 1:3 (1994), 199–215.
    • (1994) J. Comput. Biol. , vol.1 , Issue.3 , pp. 199-215
    • Hide, W.1    Burke, J.2    Davison, D.B.3
  • 23
    • 84882954143 scopus 로고    scopus 로고
    • A novel alignment-free sequence comparison method based on the numbers of adjacent amino acids
    • Huang, D.S., Yu, H.J., A novel alignment-free sequence comparison method based on the numbers of adjacent amino acids. IEEE/ACM Trans. Comput. Biol. Bioinform. 10 (2013), 457–467.
    • (2013) IEEE/ACM Trans. Comput. Biol. Bioinform. , vol.10 , pp. 457-467
    • Huang, D.S.1    Yu, H.J.2
  • 24
    • 0025340372 scopus 로고
    • Chaos game representation of gene structure
    • Jeffrey, H.J., Chaos game representation of gene structure. Nucleic Acids Res. 18:8 (1990), 2163–2170.
    • (1990) Nucleic Acids Res. , vol.18 , Issue.8 , pp. 2163-2170
    • Jeffrey, H.J.1
  • 25
    • 0343315943 scopus 로고
    • Graph theory of enzyme kinetics: 1. steady-state reaction system
    • Jiang, S.P., Liu, W.M., Fee, C.H., Graph theory of enzyme kinetics: 1. steady-state reaction system. Sci. Sin. 22 (1979), 341–358.
    • (1979) Sci. Sin. , vol.22 , pp. 341-358
    • Jiang, S.P.1    Liu, W.M.2    Fee, C.H.3
  • 26
    • 34547844142 scopus 로고    scopus 로고
    • A statistical method for alignment-free comparison of regulatory sequences
    • Kantorovitz, M.R., Robinson, G.E., Sinha, S., A statistical method for alignment-free comparison of regulatory sequences. Bioinformatics 23 (2007), 249–255.
    • (2007) Bioinformatics , vol.23 , pp. 249-255
    • Kantorovitz, M.R.1    Robinson, G.E.2    Sinha, S.3
  • 27
  • 28
    • 84859342767 scopus 로고    scopus 로고
    • Wenxiang: a web-server for drawing wenxiang diagrams
    • Lin, W.Z., Xiao, X., Wenxiang: a web-server for drawing wenxiang diagrams. Nat. Sci. 3 (2011), 862–865.
    • (2011) Nat. Sci. , vol.3 , pp. 862-865
    • Lin, W.Z.1    Xiao, X.2
  • 29
    • 84934440705 scopus 로고    scopus 로고
    • Number of distinct sequence alignments with k-match and match sections
    • Liu, X.Q., Yang, X.H., Wang, C., Yao, Y.H., Dai, Q., Number of distinct sequence alignments with k-match and match sections. Comput. Biol. Med. 63 (2015), 287–292.
    • (2015) Comput. Biol. Med. , vol.63 , pp. 287-292
    • Liu, X.Q.1    Yang, X.H.2    Wang, C.3    Yao, Y.H.4    Dai, Q.5
  • 30
    • 84873572573 scopus 로고    scopus 로고
    • Prediction of allergenic proteins by means of the concept of chou's pseudo amino acid composition and a machine learning approach
    • Mohabatkar, H., Beigi, M.M., Abdolahi, K., Mohsenzadeh, S., Prediction of allergenic proteins by means of the concept of chou's pseudo amino acid composition and a machine learning approach. Med. Chem. 9 (2013), 133–137.
    • (2013) Med. Chem. , vol.9 , pp. 133-137
    • Mohabatkar, H.1    Beigi, M.M.2    Abdolahi, K.3    Mohsenzadeh, S.4
  • 31
    • 84899962803 scopus 로고    scopus 로고
    • Chou's pseudo amino acid composition improves sequence-based antifreeze protein prediction
    • Mondal, S., Pai, P.P., Chou's pseudo amino acid composition improves sequence-based antifreeze protein prediction. J. Theor. Biol. 356 (2014), 30–35.
    • (2014) J. Theor. Biol. , vol.356 , pp. 30-35
    • Mondal, S.1    Pai, P.P.2
  • 32
    • 84885040364 scopus 로고    scopus 로고
    • A novel method for similarity/dissimilarity analysis of protein sequences
    • Mu, Z.C., Wu, J., Zhang, Y.S., A novel method for similarity/dissimilarity analysis of protein sequences. Physica A 392 (2013), 6361–6366.
    • (2013) Physica A , vol.392 , pp. 6361-6366
    • Mu, Z.C.1    Wu, J.2    Zhang, Y.S.3
  • 33
    • 61849106565 scopus 로고    scopus 로고
    • Structure and function of plant serine/arginine-rich proteins and roles in plant development
    • Na, H.Y., Deng, Z.H., Zhang, M.Q., Chen, R.K., 2008. Structure and function of plant serine/arginine-rich proteins and roles in plant development 44(6), 1209–1215. http://dx.doi.org/10.13592/j.cnki.ppj.
    • (2008) , vol.44 , Issue.6 , pp. 1209-1215
    • Na, H.Y.1    Deng, Z.H.2    Zhang, M.Q.3    Chen, R.K.4
  • 34
    • 0022631926 scopus 로고
    • The folding type of a protein is relevant to the amino acid composition
    • Nakashima, H., Nishikawa, K., Ooi, T., The folding type of a protein is relevant to the amino acid composition. J. Biochem. 99 (1986), 152–162.
    • (1986) J. Biochem. , vol.99 , pp. 152-162
    • Nakashima, H.1    Nishikawa, K.2    Ooi, T.3
  • 35
    • 0014757386 scopus 로고
    • A general method applicable to the search for similarities in the amino acid sequence of two proteins
    • Needleman, S.B., Wunsch, C.D., A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol. 48 (1970), 443–453.
    • (1970) J. Mol. Biol. , vol.48 , pp. 443-453
    • Needleman, S.B.1    Wunsch, C.D.2
  • 36
    • 12344295510 scopus 로고    scopus 로고
    • A probabilistic measure for alignment-free sequence comparison
    • Pham, T.D., Zuegg, J., A probabilistic measure for alignment-free sequence comparison. Bioinformatics 20 (2004), 3455–3461.
    • (2004) Bioinformatics , vol.20 , pp. 3455-3461
    • Pham, T.D.1    Zuegg, J.2
  • 37
    • 84955601363 scopus 로고    scopus 로고
    • An intuitive graphical method for visualizing protein sequences base on linear regression and physicochemical properties
    • Qi, Z.H., Jin, M.Z., An intuitive graphical method for visualizing protein sequences base on linear regression and physicochemical properties. MATCH Commun., Math. Comput. Chem. 75 (2016), 463–480.
    • (2016) MATCH Commun., Math. Comput. Chem. , vol.75 , pp. 463-480
    • Qi, Z.H.1    Jin, M.Z.2
  • 38
    • 70349613231 scopus 로고    scopus 로고
    • FoldRate: a web-server for predicting protein folding rates from primary sequence
    • Shen, H.B., FoldRate: a web-server for predicting protein folding rates from primary sequence. Open. Bioinforma. J. 3 (2009), 31–50.
    • (2009) Open. Bioinforma. J. , vol.3 , pp. 31-50
    • Shen, H.B.1
  • 39
    • 84900836214 scopus 로고    scopus 로고
    • New developments of alignment-free sequence comparison: measures, statistics and next-generation sequencing
    • Song, K., Ren, J., Reinert, G., Deng, M., Waterman, M.S., Sun, F., New developments of alignment-free sequence comparison: measures, statistics and next-generation sequencing. Briefings Bioinforma. 15:3 (2014), 343–353.
    • (2014) Briefings Bioinforma. , vol.15 , Issue.3 , pp. 343-353
    • Song, K.1    Ren, J.2    Reinert, G.3    Deng, M.4    Waterman, M.S.5    Sun, F.6
  • 40
    • 84955602033 scopus 로고    scopus 로고
    • A novel method of 2D graphical representation for proteins and its application
    • Sun, D., Xu, C., Zhang, Y., A novel method of 2D graphical representation for proteins and its application. MATCH Commun. Math. Comput. Chem. 75 (2016), 431–446.
    • (2016) MATCH Commun. Math. Comput. Chem. , vol.75 , pp. 431-446
    • Sun, D.1    Xu, C.2    Zhang, Y.3
  • 41
    • 33646005790 scopus 로고    scopus 로고
    • The average common substring approach to phylogenomic reconstruction
    • Ulitsky, I., Burnstein, D., Tuller, T., Chor, B., The average common substring approach to phylogenomic reconstruction. J. Comput. Bio. 13 (2006), 336–350.
    • (2006) J. Comput. Bio. , vol.13 , pp. 336-350
    • Ulitsky, I.1    Burnstein, D.2    Tuller, T.3    Chor, B.4
  • 42
    • 0037342499 scopus 로고    scopus 로고
    • Alignment-free sequence comparison—a review
    • Vinga, S., Almeida, J., Alignment-free sequence comparison—a review. Bioinformatics 19 (2003), 513–523.
    • (2003) Bioinformatics , vol.19 , pp. 513-523
    • Vinga, S.1    Almeida, J.2
  • 44
    • 84931269083 scopus 로고    scopus 로고
    • Comparative analysis of protein primary sequences with graph energy
    • Wu, H.Y., Zhang, Y.S., Chen, W., Mu, Z.C., Comparative analysis of protein primary sequences with graph energy. Physica A 437 (2015), 249–262.
    • (2015) Physica A , vol.437 , pp. 249-262
    • Wu, H.Y.1    Zhang, Y.S.2    Chen, W.3    Mu, Z.C.4
  • 45
    • 77955673069 scopus 로고    scopus 로고
    • 2D-MH: a web-server for generating graphic representation of protein sequences based on the physicochemical properties of their constituent amino acids
    • Wu, Z.C., Xiao, X., Chou, K.C., 2D-MH: a web-server for generating graphic representation of protein sequences based on the physicochemical properties of their constituent amino acids. J. Theor. Biol. 267 (2010), 29–34.
    • (2010) J. Theor. Biol. , vol.267 , pp. 29-34
    • Wu, Z.C.1    Xiao, X.2    Chou, K.C.3
  • 46
    • 20344364176 scopus 로고    scopus 로고
    • An application of gene comparative image for predicting the effect on replication ratio by HBV virus gene missense mutation
    • Xiao, X., Shao, S., Ding, Y., Huang, Z., An application of gene comparative image for predicting the effect on replication ratio by HBV virus gene missense mutation. J. Theor. Biol. 235 (2005), 555–565.
    • (2005) J. Theor. Biol. , vol.235 , pp. 555-565
    • Xiao, X.1    Shao, S.2    Ding, Y.3    Huang, Z.4
  • 47
    • 33344460430 scopus 로고    scopus 로고
    • A probability cellular automaton model for hepatitis B viral infections
    • Xiao, X., Shao, S.H., A probability cellular automaton model for hepatitis B viral infections. Biochem Biophys. Res. Comm. (BBRC) 342 (2006), 605–610.
    • (2006) Biochem Biophys. Res. Comm. (BBRC) , vol.342 , pp. 605-610
    • Xiao, X.1    Shao, S.H.2
  • 48
    • 77953039087 scopus 로고    scopus 로고
    • Similarity/dissimilarity studies of protein sequences based on a new 2D graphical representation
    • Yao, Y.H., Dai, Q., Li, L., Nan, X.Y., He, P.A., Zhang, Y.Z., Similarity/dissimilarity studies of protein sequences based on a new 2D graphical representation. J. Comput. Chem. 31 (2010), 1045–1052.
    • (2010) J. Comput. Chem. , vol.31 , pp. 1045-1052
    • Yao, Y.H.1    Dai, Q.2    Li, L.3    Nan, X.Y.4    He, P.A.5    Zhang, Y.Z.6
  • 49
    • 43249097631 scopus 로고    scopus 로고
    • A protein map and its application
    • Yau, S.S.-T., Yu, C., He, R., A protein map and its application. DNA Cell. Biol. 27 (2008), 241–250.
    • (2008) DNA Cell. Biol. , vol.27 , pp. 241-250
    • Yau, S.S.-T.1    Yu, C.2    He, R.3
  • 50
    • 84860389050 scopus 로고    scopus 로고
    • An alignment-free sequence comparison method based on various properties of amino acids
    • Yu, C.L., Cheng, S.Y., He, R.L., Yan, S.S.-T., An alignment-free sequence comparison method based on various properties of amino acids. Gene 486 (2011), 110–118.
    • (2011) Gene , vol.486 , pp. 110-118
    • Yu, C.L.1    Cheng, S.Y.2    He, R.L.3    Yan, S.S.-T.4
  • 51
    • 79551496637 scopus 로고    scopus 로고
    • DNA sequence comparison by a novel probabilistic method
    • Yu, C.L., Deng, M., Yau, S.S.-T., DNA sequence comparison by a novel probabilistic method. Inf. Sci. 181 (2011), 1484–1492.
    • (2011) Inf. Sci. , vol.181 , pp. 1484-1492
    • Yu, C.L.1    Deng, M.2    Yau, S.S.-T.3
  • 52
    • 79957601831 scopus 로고    scopus 로고
    • A novel 2D graphical representation of protein sequence based on individual amino acid
    • Yu, J.F., Sun, X., Wang, J.H., A novel 2D graphical representation of protein sequence based on individual amino acid. Int. J. Quant. Chem. 111 (2011), 2835–2843.
    • (2011) Int. J. Quant. Chem. , vol.111 , pp. 2835-2843
    • Yu, J.F.1    Sun, X.2    Wang, J.H.3
  • 53
    • 0027312593 scopus 로고
    • Graphic analysis of codon usage strategy in 1490 human proteins
    • Zhang, C.T., Graphic analysis of codon usage strategy in 1490 human proteins. J. Protein Chem. 12 (1993), 329–335.
    • (1993) J. Protein Chem. , vol.12 , pp. 329-335
    • Zhang, C.T.1
  • 54
    • 0028237028 scopus 로고
    • Analysis of codon usage in 1562 E. Coli protein coding sequences
    • Zhang, C.T., Analysis of codon usage in 1562 E. Coli protein coding sequences. J. Mol. Biol. 238 (1994), 1–8.
    • (1994) J. Mol. Biol. , vol.238 , pp. 1-8
    • Zhang, C.T.1
  • 55
    • 79959575331 scopus 로고    scopus 로고
    • A new measure for similarity searching in DNA sequences
    • Zhang, Y.S., Chen, W., A new measure for similarity searching in DNA sequences. MATCH Commun., Math. Comput. Chem. 65 (2011), 477–488.
    • (2011) MATCH Commun., Math. Comput. Chem. , vol.65 , pp. 477-488
    • Zhang, Y.S.1    Chen, W.2
  • 56
    • 84908544636 scopus 로고    scopus 로고
    • Molecular science for drug development and biomedicine
    • Zhong, W.Z., Zhou, S.F., Molecular science for drug development and biomedicine. Int. J. Mol. Sci. 15 (2014), 20072–20078.
    • (2014) Int. J. Mol. Sci. , vol.15 , pp. 20072-20078
    • Zhong, W.Z.1    Zhou, S.F.2
  • 57
    • 0021764092 scopus 로고
    • An extension of Chou's graphic rules for deriving enzyme kinetic equations to systems involving parallel reaction pathways
    • Zhou, G.P., Deng, M.H., An extension of Chou's graphic rules for deriving enzyme kinetic equations to systems involving parallel reaction pathways. Biochem. J. 222 (1984), 169–176.
    • (1984) Biochem. J. , vol.222 , pp. 169-176
    • Zhou, G.P.1    Deng, M.H.2
  • 58
    • 79960604768 scopus 로고    scopus 로고
    • The disposition of the LZCC protein residues in wenxiang diagram provides new insights into the protein-protein interaction mechanism
    • Zhou, G.P., The disposition of the LZCC protein residues in wenxiang diagram provides new insights into the protein-protein interaction mechanism. J. Theor. Biol. 284 (2011), 142–148.
    • (2011) J. Theor. Biol. , vol.284 , pp. 142-148
    • Zhou, G.P.1
  • 59
    • 84878778648 scopus 로고    scopus 로고
    • The pH-triggered conversion of the PrP(c) to PrP(sc.)
    • Zhou, G.P., Huang, R.B., The pH-triggered conversion of the PrP(c) to PrP(sc.). Curr. Top. Med Chem. 13 (2013), 1152–1163.
    • (2013) Curr. Top. Med Chem. , vol.13 , pp. 1152-1163
    • Zhou, G.P.1    Huang, R.B.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.