Comparative analysis of the base composition and codon usages in fourteen mycobacteriophage genomes

Journal of Biomolecular Structure and Dynamics

Volumn 23, Issue 1, 2005, Pages 63-71

  Sahu, K ^a   Gupta, S K ^a   Sau, S ^b   Ghosh, T C ^a  

^a Bioinformatics Centre   (India)

^b BOSE INSTITUTE   (India)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BACTERIOPHAGE; CLUSTER ANALYSIS; CODON USAGE; COMPARATIVE STUDY; DNA BASE COMPOSITION; GC RICH SEQUENCE; GENE EXPRESSION; GENOME; MUTATION; MYCOBACTERIOPHAGE SMEGMATIS; NONHUMAN; PRIORITY JOURNAL; RNA TRANSLATION;

EID: 20944451749     PISSN: 07391102     EISSN: 15380254     Source Type: Journal    
DOI: 10.1080/07391102.2005.10507047     Document Type: Article

References (47)

1. Bernardi, G., and Bernardi, G., 1986. J. Mol. Evol., 24:1–11.
2. Musto, H., Naya, H., Zavala, A., Romero, H., Alvarez-Valin, F., and Bernardi, G., 2004. FEBS Letters, 573:73–77.
3. Sueoka, N., 1961. Cold Spring Harbor Symp. Quant. Biol., 26:35–43.
4. Gu, X., Hewett-Emmett, D., and Li, W-H. 1998. Genetica, 103:383–391.
5. D'Onofrio, G., and Bernardi, G., 1992. Gene, 110:81–88.
6. Majumdar, S., Gupta, S. K., Sundararajan, V. S., and Ghosh, T. C., 1999. Biochem. Biophys. Res. Commun., 266:66–71.
7. Muto, A., and Osawa, S., 1987. Proc. Natl. Acad. Sci. USA, 84:166–169.
8. Singer, G. A. C., and Hickey, D. A., 2000. Mol. Biol. Evol., 17:1581–1588.
9. Grantham, R., Gautier, C., Gouy, M., Jacobzone, M., and Mercier, R., 1981. Nucl. Acids Res., 9:r43–r74.
10. Sharp, P. M., and Cowe, E., 1991. Yeast, 7:657–678.
11. Ikemura, T., 1985. Mol. Biol. Evol., 2:13–34.
12. Lesnik, T., Solomovici, J., Deana, A., Ehrlich, R., and Reiss, C., 2000. J. Theor. Biol., 202:175–185.
13. Gupta, S. K., and Ghosh, T. C., 2001. Gene, 273:63–70.
14. Ghosh, T. C., Gupta, S. K., and Majumdar, S., 2000. Int. J. Parasitol., 30:715–722.
15. McInerney, J. O., 1998. Proc. Natl. Acad. Sci., 95:10698–10703.
16. Romero, H., Zavala, A., and Musto, H., 2000. Nucl. Acids Res., 28:2084–2090.
17. Oresisc, M., and Shalloway, D., 1998. J. Mol. Biol., 281:31–48.
18. Gupta, S. K., Majumdar, S., Bhattacharya, T. K., and Ghosh, T. C., 2000. Biochem. Biophys. Res. Commun., 269:692–696.
19. Gu, W., Zhou, T., Ma, J., Sun, X., and Lu, Z., 2004. Biosystems, 73:89–97.
20. Xie, T., and Ding, D. F., 1998. FEBS Lett., 434:93–96.
21. D'Onofrio, G., Ghosh, T. C., and Bernardi, G., 2002. Gene, 300:179–187.
22. Pedulla, M. L., Ford, M. E., Houtz, J. M., Karthikeyan, T., Wadsworth, C., Lewis, J. A., Jacobs-Sera, D., Falbo, J., Gross, J., Pannunzio, N. R., Brucker, W., Kumar, V., Kandasamy, J., Keenan, L., Bardarov, S., Kriakov, J., Lawrence, J. G., Jacobs, W. R., Jr, Hendrix, R. W., and Hatfull, G. F., 2003. Cell, 113:171–182.
23. Hatfull, G. F., 2000. Molecular Genetics of Mycobacteria, Chapter Edited by:Hatfull, G. F., and Jacob, W. R., Jr. Vol. 2, Washington D C:ASM Press. pp 37–54
24. Kunisawa, T., 2000. J. Theor. Biol., 205:167–70.
25. Sahu, K., Gupta, S. K., Sau, S., and Ghosh, T. C., 2004. J. Biochem. Mol. Biol., 37:487–492.
26. Sharp, P. M., and Li, W.-H., 1987. Nucleic Acids Res., 15:1281–1295.
27. Wright, F., 1990. Gene, 87:23–29.
28. Greenacre, M. J., 1984. Theory and Applications of Correspondence Analysis. London, UK:Academic Press.
29. Kunisawa, T., 1998. DNA Res., 5:319–326.
30. Gouy, M., 1987. Mol. Biol. Evol., 4:426–444.
31. Sharp, P. M., Rogers, M. S., and McConnell, D. J., J. Mol. Evol., 21150–60. (1984–85)
32. Holm, L., 1986. Nucleic Acids Res., 7:3075–3087.
33. Levine, D. B., and Whitemore, B., 2000. J. Gen. Virol., 81:2313–2325.
34. Gu, W., Zhou, T., Ma, J., Sun, X., and Lu, Z., 2004. Virus Research., 101:155–161.
35. Kanaya, S., Yamada, Y., Kudo, Y., and Ikemura, T., 1999. Gene., 238:143–55.
36. Kanaya, S., Yamada, Y., Kinouchi, M., Kudo, Y., and Ikemura, T., 2001. J. Mol. Evol., 53:290–298.
37. Ikemura, T., 1992. Transfer RNA in Protein Synthesis. Ann Arbor, London, Tokyo:CRC Press.
38. Zhou, J., Liu, W. J., Peng, S. W., Sun, X. Y., and Frazer, I., 1999. J. Virol., 73:4972–4982.
39. Kropinski, A. M., and Sibbald, M. J., 1999. Can. J. Microbiol., 45:791–796.
40. Sokal, R. R., and Sneath, P. H. A., 1973. Principles of Numerical Taxonomy. W. H. Freeman San Fransisco.
41. Timme, T. L., and Brennan, P. J., 1984. J. Gen. Microbiol., 130:2059–2066.
42. Talarico, L. A., Ingram, L. O., and Maupin-Furlow, J. A., 2001. Microbiology, 147:2425–2435.
43. Sharp, P. M., Tuohy, T. M., and Mosurski, K. R., 1986. Nucleic Acids Res., 14:5125–5143.
44. Ma, J., Zhou, T., Gu, W., Sun, X., and Lu, Z., 2002. Biosystems., 65:199–207.
45. Pouwels, P. H., and Leunissen, J. A., 1994. Nucleic Acids Res., 22:929–936.
46. Lynn, D. J., Singer, G. A. C., and Hickey, D. A., 2002. Nucleic Acids Res., 30:4272–4277.
47. Shepherd, J. C. W., 1981. Proc. Natl. Acad. Sci., 78:1596–1600.