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Topic: Codon usage bias

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	Codon usage bias - Wikipedia, the free encyclopedia
		Codons are triplets of nucleotides that together specify an amino acid residue in a polypeptide chain.
		It is generally acknowledged that codon preferences reflect a balance between mutational biases and natural selection for translational optimization.
		In other organisms that do not show high growing rates, or that present small genomes, codon usage optimization is normally absent, and codon preferences are determined by the characteristic mutational biases seen in that particular genome.
	www.wikipedia.org /wiki/Codon_usage_bias (409 words)

	P450 CODON USAGE RESULTS
		was estimated by summing the usage of the preferred codon for each of the 18 amino acids for which synonymous codons exist and expressing it as a percentage of all the synonymous codons in that gene.
		In the above figure codon usage bias (the tendency to use a limited subset of codons) is plotted against the estimated evolutionary distance of 18 P450 subfamilies.
		This graph demonstrates that preferred P450 codons in these four mammals usually end in C or G. In the figure above codon usage bias is plotted against codon 3rd position C+G content for each of the 110 genes analyzed in this study.
	www.uky.edu /Pharmacy/ps/porter/CodonUsage/p450_codon_usage_results.htm (1020 words)

	"Evolution of codon usage bias in Drosophila " (Site not responding. Last check: 2007-10-13)
		"Evolution of codon usage bias in Drosophila "
		We then examine possible causes of these patterns and discount mutation bias on three bases: there is little evidence of regional mutation bias in Drosophila, mutation bias is likely toward A+T (the opposite of codon usage bias), and not all amino acids display the preference for the same nucleotide in the wobble position.
		Finally, we examine the effect of bias on DNA evolution and confirm that genes with high codon usage bias have lower rates of synonymous substitution between species than do genes with low codon usage bias.
	www.biotech-info.net /evolution_codon.html (340 words)

	BioMed Central \| Full text \| Quantitative relationship between synonymous codon usage bias and GC composition across ...
		Previous codon usage analyses showed that codon usage bias is very complicated and is associated with various biological factors, such as gene expression level [7-10], gene length [11-13], gene translation initiation signal [14], protein amino acid composition [6,15], protein structure [16,17], tRNA abundance [18-21], mutation frequency and patterns [22,23], and GC composition [24-27].
		It may be interesting to investigate the relationships between those reported gene features [7-27] and codon usage bias of those horizontally transferred genes in their new adapted hosts.
		In summary, we developed a simple binary selection model that mimicked the quantitative relationship between the codon usage bias and GC composition in the unicellular organisms, which was supported by systematically characterizing the relationship between codon usage bias and GC composition among 86 unicellular organisms.
	www.biomedcentral.com /1471-2148/4/19 (4381 words)

	General Codon Usage Analysis Homepage (Site not responding. Last check: 2007-10-13)
		RSCU values are the number of times a particular codon is observed, relative to the number of times that the codon would be observed in the absence of any codon usage bias.
		It then divides this number by the number of codons for the amino acid (2,3,4 or 6), this gives the expected number of times that the codons should be observed.
		It makes the codon usage value independent of amino acid composition of the sequences and identifies when a codon is being used more frequently than expected and when it is being used less frequently than expected.
	bioinf.may.ie /gcua/calculatecodon.html (537 words)

	Absence of translationally selected synonymous codon usage bias in Helicobacter pylori -- Lafay et al. 146 (4): 851 -- ...
		of codon usage appear to be dominated by strong mutational biases.
		) and this is reflected in codon usage.
		Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes: a proposal for a synonymous codon choice that is optimal for the E.
	mic.sgmjournals.org /cgi/content/full/146/4/851 (5188 words)

	Evolution of codon usage bias in Drosophila -- Powell and Moriyama 94 (15): 7784 -- Proceedings of the National ...
		evidence that mutation bias is the cause of codon usage bias in
		The numbers shown are the correlation coefficients between the degree of codon usage bias of the individual amino acid, ENC-X, and the frequency of the base in the third position.
		melanogaster correlate with the degree of codon bias?
	www.pnas.org /cgi/content/full/94/15/7784 (4690 words)

	BioMed Central \| Abstract \| Quantitative relationship between synonymous codon usage bias and GC composition across ...
		Codon usage bias has been widely reported to correlate with GC composition.
		However, the quantitative relationship between codon usage bias and GC composition across species has not been reported.
		The parameters within this model were inferred by inspecting the relationship between codon usage bias and GC composition across 70 bacterial and 16 archaeal genomes.
	www.biomedcentral.com /1471-2148/4/19/abstract (286 words)

	Summary of the 2000-2005 research activity of the Genetics of Bacterial Genomes unit
		A second bias is imposed by the G+C content of the genome, acting at the first codon position, indicating that protein functions are so robust with respect to amino acid changes that they can accommodate a large shift in the nucleotide content of the genome.
		There is such a strong bias in one strand as compared to the other (the leading strand is G+T-rich, while the lagging strand is A+C-rich), that the bias is reflected in the amino acid composition of the proteins encoded by each strand (valine-rich for the leading strand, isoleucine+threonine-rich for the lagging strand)!
		This bias is not present in all genomes (it seems to be absent from genomes of bacteria having an important proportion of membranes, such as the methanogens or the cyanobacteria), but, when present, it is universally the same.
	www.pasteur.fr /recherche/unites/REG/Summary.html (13079 words)

	Graphical Codon Usage Analyser
		Differences in codon usage among organisms can lead to a variety of problems concerning heterologous gene expression.
		The sequence will be splitted in codons and the fraction of usage of each codon in the selected organism will be represented as one column.
		The fraction of usage of each codon in the submitted sequence will be computed and plotted against the fraction of usage of the codon in the selected organism.
	gcua.schoedl.de (145 words)

	Accounting for Background Nucleotide Composition When Measuring Codon Usage Bias -- Novembre 19 (8): 1390 -- Molecular ...
		inversely proportional to the extent of nonuniform codon usage.
		Sharp P., W. Li, 1987 The rate of synonymous substitution in enterobacterial genes is inversely related to codon usage bias Mol.
		Synonymous codon bias is not caused by mutation bias in G+C-rich genes in humans Mol.
	mbe.oxfordjournals.org /cgi/content/full/19/8/1390 (2214 words)

	Intragenic Spatial Patterns of Codon Usage Bias in Prokaryotic and Eukaryotic Genomes -- Qin et al. 168 (4): 2245 -- ...
		Codon usage bias may also be influenced by the interaction of
		Intragenic spatial codon usage bias in prokaryotic genomes:
		codon positions for the first halves and second halves are presented along the translational direction.
	www.genetics.org /cgi/content/full/168/4/2245 (6326 words)

	Codon Usage Bias Covaries With Expression Breadth and the Rate of Synonymous Evolution in Humans, but This Is Not ... (Site not responding. Last check: 2007-10-13)
		Codon Usage Bias Covaries With Expression Breadth and the Rate of Synonymous Evolution in Humans, but This Is Not Evidence for Selection
		Correlation of codon usage bias using the MCB method and G + C content at third sites (GC3s), (A) assuming equiprobability and (B) correcting by nucleotide bias in a sample of 2396 human genes.
		bias covaries with breadth of expression and is inversely correlated
	intl.genetics.org /cgi/content/full/159/3/1191 (5446 words)

	Codon usage bias from tRNA's point of view: Redundancy, specialization, and efficient decoding for translation ...
		the frequency of anticodons and codon usage bias.
		Grosjean, H. and Fiers, W. Preferential codon usage in prokaryotic genes: The optimal codon-anticodon interaction energy and the selective codon usage in efficiently expressed genes.
		Jansen, R., Bussemaker, H.J., and Gerstein, M. Revisiting the codon adaptation index from a whole-genome perspective: Analyzing the relationship between gene expression and codon occurrence in yeast using a variety of models.
	www.genome.org /cgi/content/full/14/11/2279 (6055 words)

	Intragenic Spatial Patterns of Codon Usage Bias in Prokaryotic and Eukaryotic Genomes -- Qin et al. 168 (4): 2245 -- ...
		Intragenic Spatial Patterns of Codon Usage Bias in Prokaryotic and Eukaryotic Genomes -- Qin et al.
		spatial pattern of codon usage bias, with less bias in the middle
		and fruit fly, spatial patterns of codon usage bias are characteristically
	www.genetics.org /cgi/content/abstract/168/4/2245 (284 words)

	Evolution of codon usage bias in Drosophila -- Powell and Moriyama 94 (15): 7784 -- Proceedings of the National ...
		Codon bias and frequency-dependent selection on the hemagglutinin epitopes of influenza A virus
		Conserved codon composition of ribosomal protein coding genes in Escherichia coli, Mycobacterium tuberculosis and Saccharomyces cerevisiae: lessons from supervised machine learning in functional genomics
		Expression pattern and, surprisingly, gene length shape codon usage in Caenorhabditis, Drosophila, and Arabidopsis
	www.pnas.org /cgi/content/abstract/94/15/7784 (1474 words)

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