Re-prediction of protein-coding genes in the genome of Amsacta moorei entomopoxvirus

Journal of Virological Methods

Volumn 146, Issue 1-2, 2007, Pages 389-392

  Guo, Feng Biao ^a   Yu, Xiu Juan ^b  

^a UNIVERSITY OF ELECTRONIC SCIENCE AND TECHNOLOGY OF CHINA   (China)

^b SICHUAN UNIVERSITY   (China)

Author keywords

AmEPV genome; Gene recognition; Z curve

Indexed keywords

VIRUS PROTEIN;

AMSACTA MOOREI ENTOMOPOXVIRUS; ARTICLE; ENTOMOPOXVIRUS; GENETIC CONSERVATION; NONHUMAN; OPEN READING FRAME; POXVIRUS; PREDICTION; PRIORITY JOURNAL; SENSITIVITY ANALYSIS; VALIDATION PROCESS; VALIDATION STUDY; VIRUS GENE; VIRUS GENOME;

ALGORITHMS; COMPUTATIONAL BIOLOGY; DATABASES, NUCLEIC ACID; ENTOMOPOXVIRINAE; GENES, VIRAL; GENOME, VIRAL; OPEN READING FRAMES; VIRAL PROTEINS;

AMSACTA MOOREI ENTOMOPOXVIRUS 'L'; POXVIRIDAE;

EID: 35648931383     PISSN: 01660934     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jviromet.2007.07.010     Document Type: Article

References (15)

1. Afonso C.L., Tulman E.R., Lu Z., Oma E., Kutish G.F., and Rock D.L. The genome of Melanoplus sanguinipes entomopoxvirus. J. Virol. 73 (1999) 533-552
2. Barrell B.G., Air G.M., and Hutchison III C.A. Overlapping genes in bacteriophage phiX174. Nature 264 (1976) 34-41
3. Bawden A.L., Glassberg K.J., Diggans J., Shaw R., Farmerie W., and Moyer R.W. Complete genomic sequence of the Amsacta moorei entomopoxvirus: analysis and comparison with other poxviruses. Virology 274 (2000) 120-139
4. Burset M., and Guigó R. Evaluation of gene structure prediction programs. Genomics 34 (1996) 353-357
5. Cebrat S., Mackiewicz P., and Dudek M.R. The role of the genetic code in generating new coding sequences inside existing genes. Biosystems 45 (1998) 165-176
6. Chen L.L., and Zhang C.T. Seven GC-rich microbial genomes adopt similar codon usage patterns regardless of their phylogenetic lineages. Biochem. Biophys. Res. Commun. 306 (2003) 310-317
7. Da Silva M., and Upton C. Using purine skews to predict genes in AT-rich poxviruses. BMC Genomics 6 (2005) 22
8. Galperin M.Y., and Koonin E.V. Sources of systematic error in functional annotation of genomes: domain rearrangement, non-orthologous gene displacement and operon disruption. In Silico Biol. 1 (1998) 55-67
9. Gorban A.N., Zinovyev A.Y., and Popova T.G. Seven clusters in genomic triplet distributions. In Silico Biol. 3 (2003) 471-482
10. Grantham R., Gautier C., Gouy M., Mercier R., and Pave A. Codon catalog usage and the genome hypothesis. Nucleic Acids Res. 8 (1980) r49-r62
11. Guo F.B., Ou H.Y., and Zhang C.T. ZCURVE: a new system for recognizing protein-coding genes in bacterial and archaeal genomes. Nucleic Acids Res. 31 (2003) 1780-1789
12. Guo F.B., and Zhang C.T. ZCURVE_V: a new self-training system for recognizing protein-coding genes in viral and phage genomes. BMC Bioinformatics 7 (2006) 9
13. Mardia K.V., Kent J.T., and Bibby J.M. Multivariate Analysis (1979), Academic Press, London, UK
14. Ou H.Y., Guo F.B., and Zhang C.T. Analysis of nucleotide distribution in the genome of Streptomyces coelicolor A3 (2) using the Z curve method. FEBS Lett. 540 (2003) 188-194
15. Zhang C.T., and Zhang R. Analysis of distribution of bases in the coding sequences by a diagrammatic technique. Nucleic Acids Res. 19 (1991) 6313-6317