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Synonymous Codon Usage Analysis of Thirty Two Mycobacteriophage Genomes

Synonymous codon usage of protein coding genes of thirty two completely sequenced mycobacteriophage genomes was studied using multivariate statistical analysis. One of the major factors influencing codon usage is identified to be compositional bias. Codons ending with either C or G are preferred in...

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Detalles Bibliográficos
Autores principales: Hassan, Sameer, Mahalingam, Vasantha, Kumar, Vanaja
Formato: Texto
Lenguaje:English
Publicado: Hindawi Publishing Corporation 2009
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2817497/
https://www.ncbi.nlm.nih.gov/pubmed/20150956
http://dx.doi.org/10.1155/2009/316936
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author Hassan, Sameer
Mahalingam, Vasantha
Kumar, Vanaja
author_facet Hassan, Sameer
Mahalingam, Vasantha
Kumar, Vanaja
author_sort Hassan, Sameer
collection PubMed
description Synonymous codon usage of protein coding genes of thirty two completely sequenced mycobacteriophage genomes was studied using multivariate statistical analysis. One of the major factors influencing codon usage is identified to be compositional bias. Codons ending with either C or G are preferred in highly expressed genes among which C ending codons are highly preferred over G ending codons. A strong negative correlation between effective number of codons (Nc) and GC3s content was also observed, showing that the codon usage was effected by gene nucleotide composition. Translational selection is also identified to play a role in shaping the codon usage operative at the level of translational accuracy. High level of heterogeneity is seen among and between the genomes. Length of genes is also identified to influence the codon usage in 11 out of 32 phage genomes. Mycobacteriophage Cooper is identified to be the highly biased genome with better translation efficiency comparing well with the host specific tRNA genes.
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spelling pubmed-28174972010-02-11 Synonymous Codon Usage Analysis of Thirty Two Mycobacteriophage Genomes Hassan, Sameer Mahalingam, Vasantha Kumar, Vanaja Adv Bioinformatics Research Article Synonymous codon usage of protein coding genes of thirty two completely sequenced mycobacteriophage genomes was studied using multivariate statistical analysis. One of the major factors influencing codon usage is identified to be compositional bias. Codons ending with either C or G are preferred in highly expressed genes among which C ending codons are highly preferred over G ending codons. A strong negative correlation between effective number of codons (Nc) and GC3s content was also observed, showing that the codon usage was effected by gene nucleotide composition. Translational selection is also identified to play a role in shaping the codon usage operative at the level of translational accuracy. High level of heterogeneity is seen among and between the genomes. Length of genes is also identified to influence the codon usage in 11 out of 32 phage genomes. Mycobacteriophage Cooper is identified to be the highly biased genome with better translation efficiency comparing well with the host specific tRNA genes. Hindawi Publishing Corporation 2009 2010-02-01 /pmc/articles/PMC2817497/ /pubmed/20150956 http://dx.doi.org/10.1155/2009/316936 Text en Copyright © 2009 Sameer Hassan et al. https://creativecommons.org/licenses/by/3.0/ This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Hassan, Sameer
Mahalingam, Vasantha
Kumar, Vanaja
Synonymous Codon Usage Analysis of Thirty Two Mycobacteriophage Genomes
title Synonymous Codon Usage Analysis of Thirty Two Mycobacteriophage Genomes
title_full Synonymous Codon Usage Analysis of Thirty Two Mycobacteriophage Genomes
title_fullStr Synonymous Codon Usage Analysis of Thirty Two Mycobacteriophage Genomes
title_full_unstemmed Synonymous Codon Usage Analysis of Thirty Two Mycobacteriophage Genomes
title_short Synonymous Codon Usage Analysis of Thirty Two Mycobacteriophage Genomes
title_sort synonymous codon usage analysis of thirty two mycobacteriophage genomes
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2817497/
https://www.ncbi.nlm.nih.gov/pubmed/20150956
http://dx.doi.org/10.1155/2009/316936
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