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J Virol Methods. 2007 Dec;146(1-2):389-92. Epub 2007 Aug 23.

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

Author information

1
School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China. fbguo@uestc.edu.cn

Abstract

Using the Z curve method, the protein-coding genes in AmEPV genome are re-predicted. On the basis of the parameters trained on the experimentally validated genes, all of the 30 experimentally validated genes and 67 putative genes are predicted correctly as coding genes. The sensitivities of the present method for self-test and cross-validation are all 100% based on these test sets. Thirty-eight annotated conserved and hypothetical genes are predicted as non-coding ORFs. The number of re-predicted protein-coding genes in AmEPV is 256. It is significantly less than the number 294 reported in the original annotation. After extending the present method trained in AeEPV genome to the other entomopoxvirus genome, it is found that 116 of the 123 known and putative genes are predicted correctly as coding. Six of the seven falsely missed genes are less than 300bp. The present method could be extended to other poxvirus genomes with or without adaptation of training sets.

PMID:
17716751
DOI:
10.1016/j.jviromet.2007.07.010
[Indexed for MEDLINE]

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