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Topic: Codon

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	Genetic code - Wikipedia, the free encyclopedia
		For example, the codon AAU represents the amino acid asparagine (Asn), and cysteine (Cys) is represented by UGU and by UGC.
		The codon AUG both codes for methionine and serves as an initiation site: the first AUG in an mRNA's coding region is where translation into protein begins.
		Only two amino acids are specified by a single codon; one of these is the amino-acid methionine, specified by the codon AUG, which also specifies the start of transcription; the other is tryptophan, specified by the codon UGG.
	en.wikipedia.org /wiki/Codon (1987 words)

	The Genetic Code
		RNA codons occur in messenger RNA (mRNA) and are the codons that are actually "read" during the synthesis of polypeptides (the process called translation).
		These are the codons as they are read on the sense (5' to 3') strand of DNA.
		The same codons are assigned to the same amino acids and to the same START and STOP signals in the vast majority of genes in animals, plants, and microorganisms.
	users.rcn.com /jkimball.ma.ultranet/BiologyPages/C/Codons.html (620 words)

	Codon Usage
		This causes a strong codon difference bias in the second position between proteins that are essentially hydrophilic (e.g., globular) and those which are essentially hydrophobic (e.g., membrane proteins).
		Arginine, whose codons are relatively CG-rich, is a decreasing fraction of the total codons as the GC-content decreases (AT increases).
		The degree of codon bias of a gene is correlated with its rate of synonymous substitution.
	helix.biology.mcmaster.ca /721/outline2/node61.html (2329 words)

	codon on Encyclopedia.com (Site not responding. Last check: 2007-11-06)
		Codon Devices Formed by Academic and Industrial Leaders to Pursue Commercial Applications of Synthetic Biology.
		Codon 54 Polymorphism of the Fatty Acid Binding Protein 2 Gene is Associated with Increased Fat Oxidation and Hyperinsulinemia, but Not with Intestinal Fatty Acid Absorption in Korean Men.(Abstract)
		A prevalent amino acid polymorphism at codon 98 in the hepatocyte nuclear factor-1-alpha gene is associated with reduced serum C-peptide and insulin responses to an oral glucose challenge.
	www.encyclopedia.com /html/X/X-codon.asp (490 words)

	Weak selection and codon bias evolution in Drosophila
		This pattern suggests "major codon preference"; natural selection may discriminate among synonymous codons to enhance the speed or the accuracy of protein synthesis (Figure 1).
		Under major codon preference, codon usage and tRNA pools are co-adapted to enhance the efficiency of translation.
		Under major codon preference, silent DNA mutations fall into two fitness classes: "preferred" mutations that increase the number of major codons and "unpreferred" changes in the opposite direction.
	www.bio.psu.edu /faculty/akashi/weak_selec.htm (532 words)

	Survey of Synonymous Codon Usage in Nuclear Genes of Arabidopsis, Soybean, and Maize (Site not responding. Last check: 2007-11-06)
		The overall bias in synonymous codon usage of a genome is speciesspecific.
		Nuclear gene coding regions of monocots are enriched in codons ending in C and G, whereas dicots have a higher frequency of codons ending in A and U. We used a multivariate statistical analysis to examine codon usage in maize.
		In addition, consideration of G+C content or codon usage appears to be important for high levels of exp ression of bacterial genes in plants.3,4 Further systematic analyses are needed to determine the role of the G+C content and codon usage in regulating gene expression.
	www.nal.usda.gov /pgdic/Probe/v4n1_2/survey.html (434 words)

	[No title]
		Codon bias occurs when forced high-level expression of a gene with codons that are rarely used by E.
		Codon Usage in Various Organisms Codon frequencies are expressed as codons used per 1000 codons encountered.
		Codon frequencies of more than 15 codons/1000 codons are shown in bold to help identify a codon bias that may cause problems for high-level expression in E.
	www.stratagene.com /products/displayProduct.aspx?pid=608 (504 words)

	genetic code
		During protein synthesis, ribosomes move along the mRNA molecule and "read" its sequence three nucleotides at a time (codon) from the 5' end to the 3' end.
		Each amino acid is specified by the mRNA's codon, and then pairs with a sequence of three complementary nucleotides carried by a particular tRNA (anticodon).
		Since RNA is constructed from four types of nucleotides, there are 64 possible triplet sequences or codons (4x4x4).
	www.accessexcellence.org /AB/GG/genetic.html (156 words)

	Codon Intro
		Codon is a Sun Enterprise 3000 UNIX server managed by the Research Services Branch (RSB), NIMH and the Instrumentation and Computer Section, NINDS.
		Codon is available for logins from anywhere on the Internet via Telnet, or dial-in access is available using Bullwinkle, RSB's remote access server.
		Codon uses the Unix mail utility as the default user interface for mail, but Codon also offers the pine mail program from the University of Washington, which is much easier to use.
	rsb.info.nih.gov /rsb/servers/codon-into.html (993 words)

	On the Evolution of Codon Volatility -- Zhang 169 (1): 495 -- Genetics
		a gene is the average volatility for all the codons in the gene.
		codon usage of the gene from the genomic average.
		in 7740 codons, and remained unchanged in the rest of the cases.
	www.genetics.org /cgi/content/full/169/1/495 (2190 words)

	Codon usage in nucleopolyhedroviruses -- Levin and Whittome 81 (9): 2313 -- Journal of General Virology
		Codon usage in nucleopolyhedroviruses -- Levin and Whittome 81 (9): 2313 -- Journal of General Virology
		pattern with respect to synonymous codons and that genes in
		is significant variation in the codon usage of homologous genes
	vir.sgmjournals.org /cgi/content/abstract/81/9/2313 (269 words)

	Translational selection is operative for synonymous codon usage in Clostridium perfringens and Clostridium ...
		Ikemura, T. 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.
		Codon usage in Chlamydia trachomatis is the result of strand-specific mutational biases and a complex pattern of selective forces.
		Zavala, A., Naya, H., Romero, H. and Musto, H. Trends in codon and amino acid usage in Thermotoga maritima.
	mic.sgmjournals.org /cgi/content/full/149/4/855 (4288 words)

	Nonsense Mutations in Close Proximity to the Initiation Codon Fail to Trigger Full Nonsense-mediated mRNA Decay -- ...
		-globin mRNAs with nonsense mutations at codons 15 and 17 (
		Termination codons are recognized by the NMD apparatus as premature
		The relevance of the AUG proximity of a nonsense codon to NMD
	www.jbc.org /cgi/content/full/279/31/32170 (5821 words)

	Bioperl: RE: Bioperl-guts: codon bias modules - what should be in them?
		I would avoid any index that implies prior knowledge of optimal codon choice as these are species specific, and we only known this choice for very few species and it including them would seem to imply that someone would have to maintain the module with lists of optimal codons.
		The P2 statistic is quite old and I don't see it as having a general application to codon bias.
		GC-3 (GC in 3rd position) Maybe GC skew also in the 3rd codon position Relative Synonymous Codon Usage Wright's Nc Maybe Shannon triplet informational entropy and redundancy We should forget these indices are genetic code dependent so this needs to be coded for as well.
	www.bioperl.org /pipermail/bioperl-l/2000-March/003418.html (359 words)

	Codon usage in nucleopolyhedroviruses -- Levin and Whittome 81 (9): 2313 -- Journal of General Virology
		The percent frequency of all codons from the six genes (egt, fgf, pk-1, p10, p74 and polh) were plotted from the lowest to the highest occurrence within the AcMNPV genome (heavy base-line with solid squares).
		Gouy, M. and Goutier, C. Codon useage in bacteria: correlation with expressivity.
		Powell, J. and Moriyama, E. Evolution of codon bias in Drosophila.
	vir.sgmjournals.org /cgi/content/full/81/9/2313 (4207 words)

	Codon Exceptions: Selenocysteine
		The genes for glutathione peroxidase and formate dehydrogenase contain TGA codons in the middle of their coding regions (ref).
		The TGA follows the codon for the amino acid that precedes the selenocysteine in the polypeptide chain.
		In a limited number of genes, a special UGA codon, normally a termination codon, is used as a codon for the unusual amino acid selenocysteine (ref).
	opbs.okstate.edu /~melcher/MG/MGW2/MG2411.html (411 words)

	Graphical Codon Usage Analyser
		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.
		The fraction of usage of each codon in the submitted usage tables will be compared graphically.
	gcua.schoedl.de (145 words)

	Shannon Information Theoretic Computation of Synonymous Codon Usage Biases in Coding Regions of Human and Mouse Genomes ...
		The fraction of frequent codons is inversely linearly related to the fraction of rare codons (Fig.
		The rarest codon is codon 3 of leucine, and this is used
		A synonymous codon is the analogy of A, C, G, or T in the DNA multiple alignment.
	www.genome.org /cgi/content/full/12/6/944 (6210 words)

	A Role for Initiation Codon Context in Chloroplast Translation -- Esposito et al. 13 (10): 2373 -- THE PLANT CELL
		Cells were grown in TAP liquid medium at 25°C, and whole-cell proteins were separated on an SDS–polyacrylamide gel, transferred to a polyvinylidene difluoride membrane, and reacted with the antibodies indicated at left.
		Kuroda, H., and Maliga, P. Sequences downstream of the translation initiation codon are important determinants of translation efficiency in chloroplasts.
		Rimbault, B., Esposito, D., Drapier, D., Choquet, Y., Stern, D., and Wollman, F.A. Identification of the initiation codon for the atpB gene in Chlamydomonas chloroplasts excludes translation of a precursor form of the beta subunit of the ATP synthase.
	www.plantcell.org /cgi/content/full/13/10/2373 (5802 words)

	Stop codon selection in eukaryotic translation termination: comparison of the discriminating potential between human ... (Site not responding. Last check: 2007-11-06)
		The cross-linking pattern of the UGA mRNA analog in the absence of eRF1 is shown in lane 0.
		UGG codon, but not with the UCA codon (Figure 3B and C).
		Kuchino,Y., Hanyu,N., Tashiro,F. and Nishimura,S. Tetrahymena thermophila glutamine tRNA and its gene that corresponds to UAA termination codon.
	embojournal.npgjournals.com /cgi/content/full/22/7/1644 (6438 words)

	Translational recoding signals between gag and pol in diverse LTR retrotransposons -- GAO et al. 9 (12): 1422 -- RNA
		codon; (3) pol in the +1 frame relative to gag; (4) pol in the
		Codon alignments of retroelements with similar -1 frame cassettes in the overlap region between gag and pol.
		Gramstat, A., Prufer, D., and Rohde, W. The nucleic acid-binding zinc finger protein of potato virus M is translated by internal initiation as well as by ribosomal frameshifting involving a shifty stop codon and a novel mechanism of P-site slippage.
	www.rnajournal.org /cgi/content/full/9/12/1422 (4717 words)

	Replicational and transcriptional selection on codon usage in Borrelia burgdorferi -- McInerney 95 (18): 10698 -- ...
		codon to translate its corresponding amino acid (16).
		An examination of where the codons were located on the principle CA axis showed that they were not separated as clearly as
		Strand asymmetry and codon usage bias in the chloroplast genome of Euglena gracilis
	www.pnas.org /cgi/content/full/95/18/10698 (3513 words)

	Endless possibilities: translation termination and stop codon recognition -- Bertram et al. 147 (2): 255 -- Microbiology
		at UAA and UAG codons, and RF2 at UAA and UGA codons (Craigen
		codons is an integral part of the control of gene expression.
		Cis-acting factors which influence termination efficiency include the nucleotides immediately downstream of the stop codon, particularly at the +1 and +3 positions, the stop codon itself, the P-site tRNA, and the ultimate and penultimate amino acids in the nascent polypeptide chain (dark grey arrows).
	mic.sgmjournals.org /cgi/content/full/147/2/255 (7146 words)

	Codon Usage Bias Covaries With Expression Breadth and the Rate of Synonymous Evolution in Humans, but This Is Not ...
		Codon Usage Bias Covaries With Expression Breadth and the Rate of Synonymous Evolution in Humans, but This Is Not Evidence for Selection -- Urrutia and Hurst 159 (3): 1191 -- Genetics
		Codon Usage Bias Covaries With Expression Breadth and the Rate of Synonymous Evolution in Humans, but This Is Not Evidence for Selection
		alternative codons is observed, the bias is attributed to the
	www.genetics.org /cgi/content/abstract/159/3/1191 (567 words)

	search.cpan.org: Bio::Tools::CodonTable - Bioperl codon table object
		Codon tables are also called translation tables or genetics codes since that is what they try to represent.
		It is worth noting that, "Bacterial" codon table no. 11 produces an polypeptide that is, confusingly, identical to the standard one.
		Returns 'X' for unknown codons and an empty string for input strings that are not three characters long.
	search.cpan.org /~birney/bioperl-1.4/Bio/Tools/CodonTable.pm (976 words)

	OTHER RESOURCES FOR CODON USAGE ANALYSIS
		You can easily identify segments of your gene that use non-preferred codons, and also view the overall usage pattern of your gene.
		Here, for example, is the codon usage table for humans.
		You may also paste in your own sequence and generate a codon usage table, using the Countcodon program.
	www.uky.edu /Pharmacy/ps/porter/CodonUsage/Other_codon_usage_resources.htm (236 words)

	Rapid Deadenylation Triggered by a Nonsense Codon Precedes Decay of the RNA Body in a Mammalian Cytoplasmic ...
		Nonsense codon triggers accelerated deadenylation of ß-globin mRNA, preceding decay of the RNA body in the cytoplasm.
		Nonsense codon triggers accelerated deadenylation of ß-globin mRNA in the cytoplasm, preceding the decay of the mRNA body.
		The sequences encoding the translation initiation codon (ATG) and the termination codon (TGA) are indicated.
	mcb.asm.org /cgi/content/full/23/14/4805 (4722 words)

	A Role for Initiation Codon Context in Chloroplast Translation -- Esposito et al. 13 (10): 2373 -- THE PLANT CELL
		A Role for Initiation Codon Context in Chloroplast Translation -- Esposito et al.
		To study the role of initiation codon context in chloroplast
		codon may be part of a mechanism to compensate for the lack
	www.plantcell.org /cgi/content/abstract/13/10/2373 (306 words)

	General Codon Usage Analysis Homepage (Site not responding. Last check: 2007-11-06)
		This program is designed to perform various tasks that are of use for evaluating codon usage in a set of genes.
		However, the most important feature of the program is its ability to use multivariate analysis to look at variation in codon usage amongst genes.
		Although it is popular to say that an organism has a particular codon usage, it is now known that an organisms genes might have more than one codon usage pattern and it is usually only by using a multivariate analysis method that it is possible to ascertain the kinds of variation contained within the data.
	bioinf.may.ie /gcua (203 words)

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