Prediction of functional class of novel viral proteins by a statistical learning method irrespective of sequence similarity

Virology

Volumn 331, Issue 1, 2005, Pages 136-143

  Han, L Y ^a   Cai, C Z ^a,b   Ji, Z L ^c   Chen, Y Z ^a  

^a NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

^b CHONGQING UNIVERSITY   (China)

^c XIAMEN UNIVERSITY   (China)

Author keywords

Novel viral proteins; Sequence similarity; Statistical learning

Indexed keywords

ENDONUCLEASE; ENDONUCLEASE II; ENDONUCLEASE IV; ENDONUCLEASE V; EXONUCLEASE; OUTER CAPSID PROTEIN VP4; PROTEIN KINASE; RNA POLYMERASE BETA SUBUNIT; UNCLASSIFIED DRUG; VIRUS PROTEIN;

ACCURACY; AMINO ACID SEQUENCE; ARTICLE; GENE SEQUENCE; NUCLEOTIDE SEQUENCE; PREDICTION; PRIORITY JOURNAL; PROTEIN FUNCTION; STATISTICAL ANALYSIS;

ARTIFICIAL INTELLIGENCE; DATABASES, PROTEIN; MODELS, STATISTICAL; SEQUENCE ANALYSIS, PROTEIN; SEQUENCE HOMOLOGY, AMINO ACID; SOFTWARE; VIRAL PROTEINS;

CHEN;

EID: 9944245963     PISSN: 00426822     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.virol.2004.10.020     Document Type: Article

References (56)

1. M.H. Alaoui-Ismaili, and C.D. Richardson Identification and characterization of a filament-associated protein encoded by Amsacta moorei entomopoxvirus J. Virol. 70 5 1996 2697 2705
2. S.F. Altschul, T.L. Madden, A.A. Schaffer, J. Zhang, Z. Zhang, W. Miller, and D.J. Lipman Gapped BLAST and PSI-BLAST: a new generation of protein database search programs Nucleic Acids Res. 25 17 1997 3389 3402
3. S.A. Benner, S.G. Chamberlin, D.A. Liberles, S. Govindarajan, and L. Knecht Functional inferences from reconstructed evolutionary biology involving rectified databases-an evolutionarily grounded approach to functional genomics Res. Microbiol. 151 2 2000 97 106
4. J.R. Bock, and D.A. Gough Predicting protein-protein interactions from primary structure Bioinformatics 17 5 2001 455 460
5. B. Boeckmann, A. Bairoch, R. Apweiler, M.C. Blatter, A. Estreicher, E. Gasteiger, M.J. Martin, K. Michoud, C. O'Donovan, I. Phan, S. Pilbout, and M. Schneider The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003 Nucleic Acids Res. 31 1 2003 365 370
6. J. Broida, and J. Abelson Sequence organization and control of transcription in the bacteriophage T4 tRNA region J. Mol. Biol. 185 3 1985 545 563
7. C. Burges A tutorial on support vector machine for pattern recognition Data Min. Knowl. Disc. 2 1998 121 167
8. Y.D. Cai, X.J. Liu, X.B. Xu, and K.C. Chou Support vector machines for predicting HIV protease cleavage sites in protein J. Comput. Chem. 23 2 2002 267 274
9. C.Z. Cai, L.Y. Han, Z.L. Ji, X. Chen, and Y.Z. Chen SVM-Prot: web-based support vector machine software for functional classification of a protein from its primary sequence Nucleic Acids Res. 31 13 2003 3692 3697
10. C.Z. Cai, L.Y. Han, Z.L. Ji, and Y.Z. Chen Enzyme family classification by support vector machines Proteins 55 1 2004 66 76
11. F.K. Chu, G.F. Maley, D.K. West, M. Belfort, and F. Maley Characterization of the intron in the phage T4 thymidylate synthase gene and evidence for its self-excision from the primary transcript Cell 45 2 1986 157 166
12. J.A. Di Gennaro, N. Siew, B.T. Hoffman, L. Zhang, J. Skolnick, L.I. Neilson, and J.S. Fetrow Enhanced functional annotation of protein sequences via the use of structural descriptors J. Struct. Biol. 134 2-3 2001 232 245
13. C.H. Ding, and I. Dubchak Multi-class protein fold recognition using support vector machines and neural networks Bioinformatics 17 4 2001 349 358
14. J.J. Dunn, and F.W. Studier Complete nucleotide sequence of bacteriophage T7 DNA and the locations of T7 genetic elements J. Mol. Biol. 166 4 1983 477 535
15. J.A. Eisen Phylogenomics: improving functional predictions for uncharacterized genes by evolutionary analysis Genome Res. 8 3 1998 163 167
16. A.J. Enright, and C.A. Ouzounis GeneRAGE: a robust algorithm for sequence clustering and domain detection Bioinformatics 16 5 2000 451 457
17. A.J. Enright, I. Iliopoulos, N.C. Kyrpides, and C.A. Ouzounis Protein interaction maps for complete genomes based on gene fusion events Nature 402 6757 1999 86 90
18. A.J. Enright, S. Van Dongen, and C.A. Ouzounis An efficient algorithm for large-scale detection of protein families Nucleic Acids Res. 30 7 2002 1575 1584
19. D. Esposito, W.P. Fitzmaurice, R.C. Benjamin, S.D. Goodman, A.S. Waldman, and J.J. Scocca The complete nucleotide sequence of bacteriophage HP1 DNA Nucleic Acids Res. 24 12 1996 2360 2368
20. K.L. Fries, T.B. Sculley, J. Webster-Cyriaque, P. Rajadurai, R.H. Sadler, and N. Raab-Traub Identification of a novel protein encoded by the BamHI A region of the Epstein-Barr virus J. Virol. 71 4 1997 2765 2771
21. Y. Fujiwara, and M. Asogawa Protein function prediction using hidden Markov models and neural networks NEC Res. Dev. 43 2002 238 241
22. J.S. Gerber, and D.M. Hinton An N-terminal mutation in the bacteriophage T4 motA gene yields a protein that binds DNA but is defective for activation of transcription J. Bacteriol. 178 21 1996 6133 6139
23. L.Y. Han, C.Z. Cai, S.L. Lo, M.C. Chung, and Y.Z. Chen Prediction of RNA-binding proteins from primary sequence by a support vector machine approach RNA 10 3 2004 355 368
24. M.E. Hardy, M. Gorziglia, and G.N. Woode Amino acid sequence analysis of bovine rotavirus B223 reveals a unique outer capsid protein VP4 and confirms a third bovine VP4 type Virology 191 1 1992 291 300
25. R. He, F. Dobie, M. Ballantine, A. Leeson, Y. Li, N. Bastien, T. Cutts, A. Andonov, J. Cao, T.F. Booth, F.A. Plummer, S. Tyler, L. Baker, and X. Li Analysis of multimerization of the SARS coronavirus nucleocapsid protein Biochem. Biophys. Res. Commun. 316 2 2004 476 483
26. S. Henikoff, E.A. Greene, S. Pietrokovski, P. Bork, T.K. Attwood, and L. Hood Gene families: the taxonomy of protein paralogs and chimeras Science 278 5338 1997 609 614
27. E.A. Herniou, J.A. Olszewski, J.S. Cory, and D.R. O'Reilly The genome sequence and evolution of baculoviruses Annu. Rev. Entomol. 48 2003 211 234
28. H.C. Hodges, and J.W. Tsai 3D-Motifs: an informatics approach to protein function prediction FASEB J. 16 2002 A543
29. S. Hua, and Z. Sun A novel method of protein secondary structure prediction with high segment overlap measure: support vector machine approach J. Mol. Biol. 308 2 2001 397 407
30. J.A. Hughes, L.R. Brown, and A.J. Ferro Nucleotide sequence and analysis of the coliphage T3 S-adenosylmethionine hydrolase gene and its surrounding ribonuclease III processing sites Nucleic Acids Res. 15 2 1987 717 729
31. L.J. Jensen, R. Gupta, N. Blom, D. Devos, J. Tamames, C. Kesmir, H. Nielsen, H.H. Staerfeldt, K. Rapacki, C. Workman, C.A. Andersen, S. Knudsen, A. Krogh, A. Valencia, and S. Brunak Prediction of human protein function from post-translational modifications and localization features J. Mol. Biol. 319 5 2002 1257 1265
32. R. Karchin, K. Karplus, and D. Haussler Classifying G-protein coupled receptors with support vector machines Bioinformatics 18 1 2002 147 159
33. H.R. Luttichau, I. Clark-Lewis, P.O. Jensen, C. Moser, J. Gerstoft, and T.W. Schwartz A highly selective CCR2 chemokine agonist encoded by human herpesvirus 6 J. Biol. Chem. 278 13 2003 10928 10933
34. E.V. Makeyev, and D.H. Bamford Evolutionary potential of an RNA virus J. Virol. 78 4 2004 2114 2120
35. E.M. Marcotte, M. Pellegrini, H.L. Ng, D.W. Rice, T.O. Yeates, and D. Eisenberg Detecting protein function and protein-protein interactions from genome sequences Science 285 5428 1999 751 753
36. M.A. Marra, S.J. Jones, C.R. Astell, R.A. Holt, A. Brooks-Wilson, Y.S. Butterfield, J. Khattra, J.K. Asano, S.A. Barber, S.Y. Chan, A. Cloutier, S.M. Coughlin, D. Freeman, N. Girn, O.L. Griffith, S.R. Leach, M. Mayo, H. McDonald, S.B. Montgomery, P.K. Pandoh, A.S. Petrescu, A.G. Robertson, J.E. Schein, A. Siddiqui, D.E. Smailus, J.M. Stott, G.S. Yang, F. Plummer, A. Andonov, H. Artsob, N. Bastien, K. Bernard, T.F. Booth, D. Bowness, M. Czub, M. Drebot, L. Fernando, R. Flick, M. Garbutt, M. Gray, A. Grolla, S. Jones, H. Feldmann, A. Meyers, A. Kabani, Y. Li, S. Normand, U. Stroher, G.A. Tipples, S. Tyler, R. Vogrig, D. Ward, B. Watson, R.C. Brunham, M. Krajden, M. Petric, D.M. Skowronski, C. Upton, and R.L. Roper The genome sequence of the SARS-associated coronavirus Science 300 5624 2003 1399 1404
37. E.S. Miller, E. Kutter, G. Mosig, F. Arisaka, T. Kunisawa, and W. Ruger Bacteriophage T4 genome Microbiol. Mol. Biol. Rev. 67 1 2003 86 156 (Table of contents)
38. S. Pande, A. Makela, S.L. Dove, B.E. Nickels, A. Hochschild, and D.M. Hinton The bacteriophage T4 transcription activator MotA interacts with the far-C-terminal region of the sigma70 subunit of Escherichia coli RNA polymerase J. Bacteriol. 184 14 2002 3957 3964
39. G. Rustici, R.G. Milne, and G.P. Accotto Nucleotide sequence, genome organisation and phylogenetic analysis of Indian citrus ringspot virus. Brief report Arch. Virol. 147 11 2002 2215 2224
40. S. Sabanadzovic, N.A. Ghanem-Sabanadzovic, P. Saldarelli, and G.P. Martelli Complete nucleotide sequence and genome organization of Grapevine fleck virus J. Gen. Virol. 82 Pt. 8 2001 2009 2015
41. F. Sanger, A.R. Coulson, G.F. Hong, D.F. Hill, and G.B. Petersen Nucleotide sequence of bacteriophage lambda DNA J. Mol. Biol. 162 4 1982 729 773
42. B.M. Sjoberg, S. Hahne, C.Z. Mathews, C.K. Mathews, K.N. Rand, and M.J. Gait The bacteriophage T4 gene for the small subunit of ribonucleotide reductase contains an intron EMBO J. 5 8 1986 2031 2036
43. P.M. Skowron, N. Swaminathan, K. McMaster, D. George, J.L. Van Etten, and D.A. Mead Cloning and applications of the two/three-base restriction endonuclease R.CviJI from IL-3A virus-infected Chlorella Gene 157 1-2 1995 37 41
44. S. Spaderna, H. Blessing, E. Bogner, W. Britt, and M. Mach Identification of glycoprotein gpTRL10 as a structural component of human cytomegalovirus J. Virol. 76 3 2002 1450 1460
45. S.A. Teichmann, A.G. Murzin, and C. Chothia Determination of protein function, evolution and interactions by structural genomics Curr. Opin. Struct. Biol. 11 3 2001 354 363
46. A.E. Todd, C.A. Orengo, and J.M. Thornton Plasticity of enzyme active sites Trends Biochem. Sci. 27 8 2002 419 426
47. J. Tomaschewski, and W. Ruger Nucleotide sequence and primary structures of gene products coded for by the T4 genome between map positions 48.266 kb and 39.166 kb Nucleic Acids Res. 15 8 1987 3632 3633
48. J. Tomaschewski, H. Gram, J.W. Crabb, and W. Ruger T4-induced alpha- and beta-glucosyltransferase: cloning of the genes and a comparison of their products based on sequencing data Nucleic Acids Res. 13 21 1985 7551 7568
49. K. Valerie, E.E. Henderson, and J.K. deRiel Identification, physical map location and sequence of the denV gene from bacteriophage T4 Nucleic Acids Res. 12 21 1984 8085 8096
50. K. Valerie, J. Stevens, M. Lynch, E.E. Henderson, and J.K. de Riel Nucleotide sequence and analysis of the 58.3 to 65.5-kb early region of bacteriophage T4 Nucleic Acids Res. 14 21 1986 8637 8654
51. F.I.J. Wilfred, E.C. Roode, R.W. Goldbach, J.M. Vlak, and D. Zuidema Characterization of Spodoptera exigua multicapsid nucleopolyhedrovirus ORF17/18, a homologue of Xestia c-nigrum granulovirus ORF129 J. Gen. Virol. 83 Pt. 11 2002 2857 2867
52. D.L. Wheeler, D.M. Church, S. Federhen, A.E. Lash, T.L. Madden, J.U. Pontius, G.D. Schuler, L.M. Schriml, E. Sequeira, T.A. Tatusova, and L. Wagner Database resources of the National Center for Biotechnology Nucleic Acids Res. 31 1 2003 28 33
53. R.J. Yanez, J.M. Rodriguez, M.L. Nogal, L. Yuste, C. Enriquez, J.F. Rodriguez, and E. Vinuela Analysis of the complete nucleotide sequence of African swine fever virus Virology 208 1 1995 249 278
54. C. Yin, J. Yu, L. Wang, Z. Li, P. Zhang, and Y. Pang Identification of a novel protein associated with envelope of occlusion-derived virus in Spodoptera litura multicapsid nucleopolyhedrovirus Virus Genes 26 1 2003 5 13
55. Z. Yuan, K. Burrage, and J.S. Mattick Prediction of protein solvent accessibility using support vector machines Proteins 48 3 2002 566 570
56. Y. Zhang, M. Nelson, J.W. Nietfeldt, D.E. Burbank, and J.L. Van Etten Characterization of Chlorella virus PBCV-1 CviAII restriction and modification system Nucleic Acids Res. 20 20 1992 5351 5356