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Letters in Organic Chemistry

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ISSN (Print): 1570-1786
ISSN (Online): 1875-6255

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Research Article

Identification of Phage Virion Proteins by Using the g-gap Tripeptide Composition

Author(s): Liangwei Yang, Hui Gao*, Zhen Liu and Lixia Tang

Volume 16, Issue 4, 2019

Page: [332 - 339] Pages: 8

DOI: 10.2174/1570178615666180910112813

Price: $65

Abstract

Phages are widely distributed in locations populated by bacterial hosts. Phage proteins can be divided into two main categories, that is, virion and non-virion proteins with different functions. In practice, people mainly use phage virion proteins to clarify the lysis mechanism of bacterial cells and develop new antibacterial drugs. Accurate identification of phage virion proteins is therefore essential to understanding the phage lysis mechanism. Although some computational methods have been focused on identifying virion proteins, the result is not satisfying which gives more room for improvement. In this study, a new sequence-based method was proposed to identify phage virion proteins using g-gap tripeptide composition. In this approach, the protein features were firstly extracted from the ggap tripeptide composition. Subsequently, we obtained an optimal feature subset by performing incremental feature selection (IFS) with information gain. Finally, the support vector machine (SVM) was used as the classifier to discriminate virion proteins from non-virion proteins. In 10-fold crossvalidation test, our proposed method achieved an accuracy of 97.40% with AUC of 0.9958, which outperforms state-of-the-art methods. The result reveals that our proposed method could be a promising method in the work of phage virion proteins identification.

Keywords: Phage virion proteins, g-gap tripeptide composition, SVM, IFS, information gain, 10-fold cross validation.

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[1]
Martelet, A.; L’hostis, G.; Tavares, P.; Brasiles, S.; Fenaille, F.; Rozand, C.; Theretz, A.; Gervasi, G.; Tablet, J.; Ezan, E. J. Proteome Res., 2014, 3, 1450-1465.
[2]
Aguilar, P.V.; Adams, A.P.; Wang, E.; Kang, W.; Carrara, A.S.; Anishchenko, M.; Frolov, L.; Weaver, S.C. J. Virol., 2008, 10, 4920-4930.
[3]
Moreland, N.J.; Tay, M.Y.F.; Lim, E.; Paradkar, P.N.; Doan, D.N.P.; Yau, Y.H.; Shochat, S.G.; Vasudevan, S.G. PLoS Negl. Trop. Dis., 2010, 11, e881.
[4]
Seguritan, V.N.; Alves, M.; Arnoult, A.; Raymond, D.; Lorimer, A.B.; Burgin Jr, P.; Salamon, A.M. PLOS Comput. Biol., 2012, 8, e1002657.
[5]
Feng, P.-M.; Ding, H.; Chen, W.; Lin, H. Comput. Math. Methods Med., 2013, 2013
[6]
Ding, H.; Feng, P-M.; Chen, W.; Lin, H. Mol. Biosyst., 2014, 10, 2229-2235.
[7]
Jia, J.; Liu, Z.; Xiao, X.; Liu, B.; Chou, K-C. J. Theor. Biol., 2015, 377, 47-56.
[8]
Li, F.; Li, C.; Marquez-lago, T.; Leier, A.; Akutsu, T.; Purcell, A.W.; Smith, A.; Lithgow, T.; Daly, R.J.; Song, J.; Chou, K.C. Bioinformatics, 2018, 34, 4223-4231.
[9]
Cheng, X.; Xiao, X.; Chou, K.C. Bioinforma. Oxf. Engl., 2017, 33, 3524-3531.
[10]
Song, J.; Li, F.; Takemoto, K.; Haffari, G.; Akutsu, T.; Chou, K.C.; Webb, G. J. Theor. Biol., 2018, 443, 125-137.
[11]
Jia, J.; Liu, Z.; Xiao, X.; Liu, B.; Chou, K-C. J. Biomol. Struct. Dyn., 2016, 34, 1946-1961.
[12]
Jia, J.; Liu, Z.; Xiao, X.; Liu, B.; Chou, K-C. Molecules, 2016, 21, 95.
[13]
Cheng, X.; Xiao, X.; Chou, K-C. Genomics, 2018, 110, 50-58.
[14]
Liu, B.; Weng, F.; Huang, D.S.; Chou, K.C. Bioinformatics, 2018, 34, 3086-3093.
[15]
Chen, W.; Feng, P.; Yang, H.; Ding, H.; Lin, H.; Chou, K-C. Mol. Ther. Nucleic Acids, 2018, 11, 468-474.
[16]
Liu, B.; Yang, F.; Huang, D.S.; Chou, K.C. Bioinformatics, 2017, 34, 33-40.
[17]
Liu, B.; Li, K.; Huang, D.S.; Chou, K.C. Bioinformatics, 2018, 34, 3835-3842.
[18]
Feng, P.; Yang, H.; Ding, H.; Lin, H.; Chen, W.; Chou, K-C. Genomics, 2018.
[19]
Chen, W.; Feng, P-M.; Lin, H.; Chou, K-C. Nucleic Acids Res., 2013, 41, e68-e68.
[20]
Song, J.; Wang, Y.; Li, F.; Akutsu, T.; Rawling, N.D.; Webb, G.I.; Chou, K.C. Brief. Bioinform., 2018.
[http://dx.doi.org/10.1093/bib/bby028]
[21]
Su, Z-D.; Huang, Y.; Zhang, Z.Y.; Zhao, Y.W.; Wang, D.; Chen, W.; Chou, K.C.; Lin, H. Bioinformatics, 2018, 34, 4196-4204.
[22]
Chou, K.C. J. Theor. Biol., 2011, 273, 236-247.
[23]
Apweiler, R.; Bairoch, A.; Wu, C.H.; Barker, W.C.; Boeckmann, B.; Ferro, S.; Gasteiger, E.; Huang, H.; Lopez, R.; Magrane, M. Nucleic Acids Res., 2004, 22, D115-D119.
[24]
Lobo, I. J. Mol. Biol., 2008, 215, 403-410.
[25]
Chou, K.C. Med. Chem., 2015, 11, 218-234.
[26]
Nakashima, H.; Nishikawa, K. J. Mol. Biol., 1994, 238, 54-61.
[27]
Chou, K-C. Proteins Struct. Funct. Bioinform., 2001, 3, 246-255.
[28]
Mandal, M.; Mukhopadhyay, A.; Maulik, U. Med. Biol. Eng. Comput., 2015, 53, 331-344.
[29]
Arif, M.; Hayat, M.; Jan, Z. J. Theor. Biol., 2018, 442, 11-21.
[30]
Mei, J.; Zhao, J. J. Theor. Biol., 2018, 447, 147.
[31]
Krishnan, S.M. J. Theor. Biol., 2018, 445, 62-74.
[32]
Rahman, M.S.; Shatabda, S.; Saha, S.; Kaykobad, M.; Rahman, M.S. J. Theor. Biol., 2018, 452, 22-34.
[33]
Sabooh, M.F.; Iqbal, N.; Khan, M.; Khan, M.; Maqbool, H.F. J. Theor. Biol., 2018, 452, 1-9.
[34]
Mei, J.; Zhao, J. Sci. Rep., 2018, 8, 2359.
[35]
Zhou, X.B.; Chen, C.; Li, Z.C.; Zou, X.Y. J. Theor. Biol., 2007, 248, 546-551.
[36]
Esmaeili, M.; Mohabatkar, H.; Mohsenzadeh, S. J. Theor. Biol., 2010, 263, 203-209.
[37]
Nanni, L.; Lumini, A.; Gupta, D.; Garg, A. IEEE/ACM Trans. Comput. Biol. Bioinformatics, 2012, 9, 467-475.
[38]
Mohammad, B.M.; Behjati, M.; Mohabatkar, H. J. Struct. Funct. Genomics, 2011, 12, 191-197.
[39]
Khan, A. Protein Pept. Lett., 2012, 19, 890-903.
[40]
Gupta, M.K.; Niyogi, R.; Misra, M. SAR QSAR Environ. Res., 2013, 24, 597.
[41]
Khosravian, M.; Faramarzi, F.K.; Beigi, M.M.; Behbahani, M.; Mohabatkar, H. Protein Pept. Lett., 2013, 20, 180-186.
[42]
Chou, K-C. Curr. Proteomics, 2009, 6, 262-274.
[43]
Dubchak, I.; Muchnik, I.; Holbrook, S.R.; Kim, S.H. Proc. Natl. Acad. Sci., 1995, 92, 8700-8704.
[44]
Wang, H.; Hu, X. BMC Bioinformatics, 2015, 16(Suppl. 12), S3.
[45]
Lai, H-Y.; Chen, X-X.; Chen, W.; Tang, H.; Lin, H. Oncotarget, 2017, 8, 28169-28175.
[46]
Liu, B.; Liu, F.; Wang, X.; Chen, J.; Fang, L.; Chou, K-C. Nucleic Acids Res., 2015, 43, W65-W71.
[47]
Quinlan, J.R. C4. 5: Programs for Machine Learning; Elsevier, 2014.
[48]
Lin, H.; Deng, E-Z.; Ding, H.; Chen, W.; Chou, K-C. Nucleic Acids Res., 2014, 42, 12961-12972.
[49]
Xu, Y.; Shao, X-J.; Wu, L-Y.; Deng, N-Y.; Chou, K-C. PeerJ, 2013, 1, e171.
[50]
Dehzangi, A.; Heffernan, R.; Sharma, A.; Lyons, J.; Paliwal, K.; Sattar, A. J. Theor. Biol., 2015, 364, 284-294.
[51]
Chen, W.; Feng, P-M.; Deng, E-Z.; Lin, H.; Chou, K-C. Anal. Biochem., 2014, 462, 76-83.
[52]
Khan, Z.U.; Hayat, M.; Khan, M.A. J. Theor. Biol., 2015, 365, 197-203.
[53]
Ding, H.; Deng, E.; Yuan, L.; Lin, H.; Chen, W.; Chou, K.C. BioMed Res. Int., 2014.
[http://dx.doi.org/10.1155/2014/286419]
[54]
Anand, A.; Suganthan, P.N. J. Theor. Biol., 2009, 259, 533-540.
[55]
Chen, C.; Chen, L.X.; Zou, X.Y.; Cai, P.X. J. Theor. Biol., 2008, 253, 388-392.
[56]
Chen, K.; Kurgan, L.A.; Ruan, J. J. Comput. Chem., 2010, 29, 1596-1604.
[57]
Park, B. Im, J.; Tuvshinjargal, N.; Lee, W.; Han, K. Comput. Methods Programs Biomed., 2014, 117, 158-167.
[58]
Rajput, A.; Gupta, A.K.; Kumar, M. PLoS One, 2015, 10, e0120066.
[59]
Xu, Y.; Wang, X.; Wang, Y.; Tian, Y.; Shao, X.; Wu, L.; Deng, N. J. Theor. Biol., 2014, 344, 78-87.
[60]
Pouzols, F.M.; Lendasse, A.; Barros, A.B. Fuzzy Sets Syst., 2010, 161, 471-497.
[61]
Tung, C.W. BMC Bioinformatics, 2011, 12, 446-446.
[62]
Mckinney, B.A.; Reif, D.M.; Rock, M.T.; Edwards, K.M.; Kingsmore, S.F.; Moore, J.H. Infect. Dis., 2006, 194, 444-453.
[63]
Chen, W.; Luo, L.; Zhang, L. Nucleic Acids Res., 2010, 38, 2788-2798.
[64]
Huang, Z.; Chen, H.; Hsu, C.J.; Chen, W.H.; Wu, S. Decis. Support Syst., 2004, 37, 543-558.
[65]
Ali, F.; Hayat, M. J. Theor. Biol., 2015, 384, 78-83.
[66]
Chou, K-C. Proteins Struct. Funct. Bioinform, 2001, 42, 136-139.
[67]
Chou, K-C. Protein Eng., 2001, 14, 75-79.
[68]
Chou, K-C. Peptides, 2001, 22, 1973-1979.
[69]
Mohabatkar, H.; Beigi, M.M.; Abdolahi, K.; Mohsenzadeh, S. Med. Chem., 2013, 9, 133-137.
[70]
Chou, K-C. Bioinformatics, 2005, 21, 10-19.
[71]
Cheng, X.; Zhao, S-G.; Xiao, X.; Chou, K-C. Bioinformatics, 2016, 33, 341-346.
[72]
Cheng, X.; Zhao, S-G.; Xiao, X.; Chou, K-C. Oncotarget, 2017, 8, 58494.
[73]
Qiu, W-R.; Sun, B-Q.; Xiao, X.; Xu, Z-C.; Chou, K-C. Bioinformatics, 2016, 32, 3116-3123.
[74]
Chou, K-C.; Shen, H-B. Nat. Sci., 2009, 1, 63.
[75]
Chou, K-C. Curr. Top. Med. Chem., 2017, 17, 2337-2358.

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