Nucleic Acids Research, 2000, Vol. 28, No. 1 292
© 2000 Oxford University Press
Codon usage tabulated from international DNA sequence databases: status for the year 2000
Laboratory of Gene Structure 2, Kazusa DNA Research Institute, 1532-3 Yana, Kisarazu, Chiba 292-0812, Japan and 1National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
The frequencies of each of the 257 468 complete protein coding sequences (CDSs) have been compiled from the taxonomical divisions of the GenBank DNA sequence database. The sum of the codons used by 8792 organisms has also been calculated. The data files can be obtained from the anonymous ftp sites of DDBJ, Kazusa and EBI. A list of the codon usage of genes and the sum of the codons used by each organism can be obtained through the web site http://www.kazusa.or.jp/codon/ . The present study also reports recent developments on the WWW site. The new web interface provides data in the CodonFrequency-compatible format as well as in the traditional table format. The use of the database is facilitated by keyword based search analysis and the availability of codon usage tables for selected genes from each species. These new tools will provide users with the ability to further analyze for variations in codon usage among different genomes.
* To whom correspondence should be addressed. Tel: +81 438 52 3935; Fax: +81 438 52 3934; Email: ynakamu@kazusa.or.jp
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M. M. Krem and E. Di Cera Conserved Ser residues, the Shutter Region, and Speciation in Serpin Evolution J. Biol. Chem., September 26, 2003; 278(39): 37810 - 37814. [Abstract] [Full Text] [PDF]
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S. Biemelt, U. Sonnewald, P. Galmbacher, L. Willmitzer, and M. Muller Production of Human Papillomavirus Type 16 Virus-Like Particles in Transgenic Plants J. Virol., September 1, 2003; 77(17): 9211 - 9220. [Abstract] [Full Text] [PDF]
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A. Sudom, R. Walters, L. Pastushok, D. Goldie, L. Prasad, L. T. J. Delbaere, and H. Goldie Mechanisms of Activation of Phosphoenolpyruvate Carboxykinase from Escherichia coli by Ca2+ and of Desensitization by Trypsin J. Bacteriol., July 15, 2003; 185(14): 4233 - 4242. [Abstract] [Full Text] [PDF]
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 S. Perlman, B. van den Hazel, J. Christiansen, S. Gram-Nielsen, C. B. Jeppesen, K. V. Andersen, T. Halkier, S. Okkels, and H. T. Schambye Glycosylation of an N-Terminal Extension Prolongs the Half-Life and Increases the in Vivo Activity of Follicle Stimulating Hormone J. Clin. Endocrinol. Metab., July 1, 2003; 88(7): 3227 - 3235. [Abstract] [Full Text] [PDF]
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M. W. Hahn, J. E. Stajich, and G. A. Wray The Effects of Selection Against Spurious Transcription Factor Binding Sites Mol. Biol. Evol., June 1, 2003; 20(6): 901 - 906. [Abstract] [Full Text] [PDF]
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 A.-N. Spiess, N. Walther, N. Muller, M. Balvers, C. Hansis, and R. Ivell SPEER--A New Family of Testis-Specific Genes from the Mouse Biol Reprod, June 1, 2003; 68(6): 2044 - 2054. [Abstract] [Full Text] [PDF]
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A. Cid-Arregui, V. Juarez, and H. z. Hausen A Synthetic E7 Gene of Human Papillomavirus Type 16 That Yields Enhanced Expression of the Protein in Mammalian Cells and Is Useful for DNA Immunization Studies J. Virol., April 15, 2003; 77(8): 4928 - 4937. [Abstract] [Full Text] [PDF]
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H. A. Hussain and J. M. Ward Enhanced Heterologous Expression of Two Streptomyces griseolus Cytochrome P450s and Streptomyces coelicolor Ferredoxin Reductase as Potentially Efficient Hydroxylation Catalysts Appl. Envir. Microbiol., January 1, 2003; 69(1): 373 - 382. [Abstract] [Full Text] [PDF]
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D. Jameson, A. P. Gibson, C. Hudelot, and P. G. Higgs OGRe: a relational database for comparative analysis of mitochondrial genomes Nucleic Acids Res., January 1, 2003; 31(1): 202 - 206. [Abstract] [Full Text] [PDF]
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B. Barcelona-Andres, A. Marina, and V. Rubio Gene Structure, Organization, Expression, and Potential Regulatory Mechanisms of Arginine Catabolism in Enterococcus faecalis J. Bacteriol., November 15, 2002; 184(22): 6289 - 6300. [Abstract] [Full Text] [PDF]
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S. Akanuma, T. Kigawa, and S. Yokoyama Combinatorial mutagenesis to restrict amino acid usage in an enzyme to a reduced set PNAS, October 15, 2002; 99(21): 13549 - 13553. [Abstract] [Full Text] [PDF]
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C. Berry, S. O'Neil, E. Ben-Dov, A. F. Jones, L. Murphy, M. A. Quail, M. T. G. Holden, D. Harris, A. Zaritsky, and J. Parkhill Complete Sequence and Organization of pBtoxis, the Toxin-Coding Plasmid of Bacillus thuringiensis subsp. israelensis Appl. Envir. Microbiol., October 1, 2002; 68(10): 5082 - 5095. [Abstract] [Full Text] [PDF]
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F. S.L. Brinkman, J. L. Blanchard, A. Cherkasov, Y. Av-Gay, R. C. Brunham, R. C. Fernandez, B. B. Finlay, S. P. Otto, B.F. F. Ouellette, P. J. Keeling, et al. Evidence That Plant-Like Genes in Chlamydia Species Reflect an Ancestral Relationship between Chlamydiaceae, Cyanobacteria, and the Chloroplast Genome Res., August 1, 2002; 12(8): 1159 - 1167. [Abstract] [Full Text] [PDF]
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G. L. Moore and C. D. Maranas eCodonOpt: a systematic computational framework for optimizing codon usage in directed evolution experiments Nucleic Acids Res., June 1, 2002; 30(11): 2407 - 2416. [Abstract] [Full Text] [PDF]
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B. Borstnik and D. Pumpernik Tandem Repeats in Protein Coding Regions of Primate Genes Genome Res., June 1, 2002; 12(6): 909 - 915. [Abstract] [Full Text] [PDF]
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F. Clark and T. A. Thanaraj Categorization and characterization of transcript-confirmed constitutively and alternatively spliced introns and exons from human Hum. Mol. Genet., February 1, 2002; 11(4): 451 - 464. [Abstract] [Full Text] [PDF]
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 D. J. Brooks and J. R. Fresco Increased Frequency of Cysteine, Tyrosine, and Phenylalanine Residues Since the Last Universal Ancestor Mol. Cell. Proteomics, February 1, 2002; 1(2): 125 - 131. [Abstract] [Full Text] [PDF]
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V. Dvornyk, A. Sirvio, M. Mikkonen, and O. Savolainen Low Nucleotide Diversity at the pal1 Locus in the Widely Distributed Pinus sylvestris Mol. Biol. Evol., February 1, 2002; 19(2): 179 - 188. [Abstract] [Full Text] [PDF]
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D. Moreira, S. Kervestin, O. Jean-Jean, and H. Philippe Evolution of Eukaryotic Translation Elongation and Termination Factors: Variations of Evolutionary Rate and Genetic Code Deviations Mol. Biol. Evol., February 1, 2002; 19(2): 189 - 200. [Abstract] [Full Text] [PDF]
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R. M. van Dam and S. R. Quake Gene Expression Analysis with Universal n-mer Arrays Genome Res., January 1, 2002; 12(1): 145 - 152. [Abstract] [Full Text] [PDF]
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