scholarly journals Analysis of factors affecting codon usage bias in human papillomavirus

2018 ◽  
Vol 9 (1) ◽  
pp. 1-9 ◽  
Author(s):  
Kamatani Takaaki ◽  
Shirota Tatsuo
Keyword(s):  
Human Papillomavirus ◽  
Codon Usage ◽  
Codon Usage Bias ◽  
Factors Affecting

Codon usage bias and A+T content variation in human papillomavirus genomes

2003 ◽  
Vol 98 (2) ◽  
pp. 95-104 ◽  
Author(s):  
Kong-Nan Zhao ◽  
Wen Jun Liu ◽  
Ian H Frazer
Keyword(s):  
Human Papillomavirus ◽  
Codon Usage ◽  
Codon Usage Bias ◽  
Content Variation

Corrigendum to “Factors affecting the codon usage bias of SRY gene across mammals” [Gene 630C (2017) 13–20]

Gene ◽  
2017 ◽  
Vol 635 ◽  
pp. 77
Author(s):  
Supriyo Chakraborty ◽  
Arif Uddin ◽  
Monisha Nath Choudhury
Keyword(s):  
Codon Usage ◽  
Codon Usage Bias ◽  
Sry Gene ◽  
Factors Affecting

scholarly journals Mutation Profiles, Glycosylation Site Distribution and Codon Usage Bias of Human Papillomavirus Type 16

Viruses ◽  
2021 ◽  
Vol 13 (7) ◽  
pp. 1281
Author(s):  
Wei Liu ◽  
Junhua Li ◽  
Hongli Du ◽  
Zhihua Ou
Keyword(s):  
Human Papillomavirus ◽  
Codon Usage ◽  
Codon Usage Bias ◽  
Vaccine Development ◽  
Surface Protein ◽  
Glycosylation Site ◽  
Protein Glycosylation ◽  
Adaptation Mechanism ◽  
Human Papillomavirus Type 16 ◽  
Glycosylation Sites

Human papillomavirus type 16 (HPV16) is the most prevalent HPV type causing cervical cancers. Herein, using 1597 full genomes, we systemically investigated the mutation profiles, surface protein glycosylation sites and the codon usage bias (CUB) of HPV16 from different lineages and sublineages. Multiple lineage- or sublineage-conserved mutation sites were identified. Glycosylation analysis showed that HPV16 lineage D contained the highest number of different glycosylation sites from lineage A in both L1 and L2 capsid proteins, which might lead to their antigenic distances between the two lineages. CUB analysis showed that the HPV16 open reading frames (ORFs) preferred codons ending with A/T. The CUB of HPV16 ORFs was mainly affected by natural selection except for E1, E5 and L2. HPV16 only shared some of the preferred codons with humans, which might help reduce competition in translational resources. These findings increase our understanding of the heterogeneity between HPV16 lineages and sublineages, and the adaptation mechanism of HPV in human cells. In summary, this study might facilitate HPV classification and improve vaccine development and application.

scholarly journals Factors Affecting Synonymous Codon Usage Bias in Chloroplast Genome ofOncidium Gower Ramsey

2011 ◽  
Vol 7 ◽  
pp. EBO.S8092 ◽  
Author(s):  
Chen Xu ◽  
Xiaoning Cai ◽  
Quanzhan Chen ◽  
Hongxia Zhou ◽  
Yao Cai ◽  
...  
Keyword(s):  
Codon Usage ◽  
Chloroplast Genome ◽  
Codon Usage Bias ◽  
Synonymous Codon ◽  
Synonymous Codon Usage ◽  
Factors Affecting ◽  
Synonymous Codon Usage Bias

Factors affecting the codon usage bias of SRY gene across mammals

Gene ◽  
2017 ◽  
Vol 630 ◽  
pp. 13-20 ◽  
Author(s):  
Supriyo Chakraborty ◽  
Arif Uddin ◽  
Monisha Nath Choudhury
Keyword(s):  
Codon Usage ◽  
Codon Usage Bias ◽  
Sry Gene ◽  
Factors Affecting

scholarly journals Patterns of genome-wide codon usage bias in tobacco, tomato and potato

2021 ◽  
Vol 35 (1) ◽  
pp. 657-664
Author(s):  
Ali Mostafa Anwar ◽  
Maha Aljabri ◽  
Mohamed El-Soda
Keyword(s):  
Codon Usage ◽  
Codon Usage Bias ◽  
Genome Wide
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