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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...
Autores principales: | , , |
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Formato: | Texto |
Lenguaje: | English |
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Hindawi Publishing Corporation
2009
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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. |
format | Text |
id | pubmed-2817497 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2009 |
publisher | Hindawi Publishing Corporation |
record_format | MEDLINE/PubMed |
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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