Analysis of Synonymous Codon Usage in the Capsid Gene UL38 of Duck Enteritis Virus

Author

Jun Xiang ; Anchun Cheng ; Mingshu Wang ; Shunchuan Zhang ; Hua Chang ; Dekang Zhu ; Renyong Jia ; Qihui Luo ; Hengmin Cui ; Yi Zhou ; Yin Wang ; Zhiwen Xu ; Zhengli Chen ; Xiaoyue Chen ; Xiaoyu Wang

Author_Institution

Avian Diseases Res. Center, Sichuan Agric. Univ., Yaan, China

fYear

2010

fDate

18-20 June 2010

Firstpage

1

Lastpage

8

Abstract

In the study, we calculated the codon usage bias in the newly identified UL38 gene of Duck Enteritis Virus (DEV) and performed a correlation analysis of codon bias of DEV UL38 gene and its host animal. There was a strong bias in the DEV UL38 gene towards the synonymous codons with A and T at the third codon position. The amino acids codon usage bias in the DEV UL38 gene was compared with other 15 reference herpesviruses, and the cluster analysis suggested that UL38 gene´s type and function also contributed to the codon usage of it. In addition, there were 42 rare condons in the ORF of the DEV UL38, and 24 codons showing distinct usage differences between DEV and E. coli, 12 codons between DEV and Homo sapiens, 25 codons between DEV and yeast.

Keywords

genetics; microorganisms; statistical analysis; DEV; E. coli; Homo sapiens; ORF; capsid gene UL38; cluster analysis; correlation analysis; duck enteritis virus; reference herpes viruses; synonymous codon usage analysis; yeast; Amino acids; Animals; Bioinformatics; Diseases; Fungi; Genomics; Humans; Laboratories; Performance analysis; Proteins;

fLanguage

English

Publisher

ieee

Conference_Titel

Bioinformatics and Biomedical Engineering (iCBBE), 2010 4th International Conference on

Conference_Location

Chengdu

ISSN

2151-7614

Print_ISBN

978-1-4244-4712-1

Electronic_ISBN

2151-7614

Type

conf

DOI

10.1109/ICBBE.2010.5516889

Filename

5516889