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Literature DB >> 6393058

A method for measuring the non-random bias of a codon usage table.

Abstract

We describe a new statistical method for measuring bias in the codon usage table of a gene. The test is based on the multinomial and Poisson distributions. The method is used to scan DNA sequences and measure the strength of codon preference. For E. Coli we show that the strength of codon preference is related to levels of gene expression. The method can also be used to compare base triplet frequencies with those expected from the base composition. This second type of codon bias test is useful for distinguishing coding from non-coding regions.

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Year: 1984 PMID： 6393058 PMCID： PMC320481 DOI： 10.1093/nar/12.24.9567

Source DB: PubMed Journal: Nucleic Acids Res ISSN： 0305-1048 Impact factor: 16.971

17 in total

1. Nucleotide sequence of bacteriophage phi X174 DNA.

Authors: F Sanger; G M Air; B G Barrell; N L Brown; A R Coulson; C A Fiddes; C A Hutchison; P M Slocombe; M Smith
Journal: Nature Date: 1977-02-24 Impact factor: 49.962

2. The arrangement of nucleotides in the coding regions of natural templates.

Authors: J Sedlácek; M Fábry; I Rychlík; D Volný; A Vítek
Journal: Mol Gen Genet Date: 1979-04-17

3. The atp operon: nucleotide sequence of the genes for the gamma, beta, and epsilon subunits of Escherichia coli ATP synthase.

Authors: M Saraste; N J Gay; A Eberle; M J Runswick; J E Walker
Journal: Nucleic Acids Res Date: 1981-10-24 Impact factor: 16.971

4. The atp operon: nucleotide sequence of the promoter and the genes for the membrane proteins, and the delta subunit of Escherichia coli ATP-synthase.

Authors: N J Gay; J E Walker
Journal: Nucleic Acids Res Date: 1981-08-25 Impact factor: 16.971

5. The atp operon: nucleotide sequence of the region encoding the alpha-subunit of Escherichia coli ATP-synthase.

Authors: N J Gay; J E Walker
Journal: Nucleic Acids Res Date: 1981-05-11 Impact factor: 16.971

6. Codon preference and its use in identifying protein coding regions in long DNA sequences.

Authors: R Staden; A D McLachlan
Journal: Nucleic Acids Res Date: 1982-01-11 Impact factor: 16.971

7. DNA sequences from the str operon of Escherichia coli.

Authors: L E Post; M Nomura
Journal: J Biol Chem Date: 1980-05-25 Impact factor: 5.157

8. Codon catalog usage is a genome strategy modulated for gene expressivity.

Authors: R Grantham; C Gautier; M Gouy; M Jacobzone; R Mercier
Journal: Nucleic Acids Res Date: 1981-01-10 Impact factor: 16.971

9. 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. coli translational system.

Authors: T Ikemura
Journal: J Mol Biol Date: 1981-09-25 Impact factor: 5.469

9. Codon usage patterns suggest independent evolution of two catabolic operons on toluene-degradative plasmid TOL pWW0 of Pseudomonas putida.

Authors: S Harayama
Journal: J Mol Evol Date: 1994-04 Impact factor: 2.395

10. Codon usage and gene expression.

Authors: L Holm
Journal: Nucleic Acids Res Date: 1986-04-11 Impact factor: 16.971

A method for measuring the non-random bias of a codon usage table.

1. Nucleotide sequence of bacteriophage phi X174 DNA.

2. The arrangement of nucleotides in the coding regions of natural templates.

3. The atp operon: nucleotide sequence of the genes for the gamma, beta, and epsilon subunits of Escherichia coli ATP synthase.

4. The atp operon: nucleotide sequence of the promoter and the genes for the membrane proteins, and the delta subunit of Escherichia coli ATP-synthase.

5. The atp operon: nucleotide sequence of the region encoding the alpha-subunit of Escherichia coli ATP-synthase.

6. Codon preference and its use in identifying protein coding regions in long DNA sequences.

7. DNA sequences from the str operon of Escherichia coli.

8. Codon catalog usage is a genome strategy modulated for gene expressivity.

9. 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. coli translational system.

10. Codon selection in yeast.

1. A new measure to study phylogenetic relations in the brown algal order Ectocarpales: the "codon impact parameter".

2. Locating protein-coding regions in human DNA sequences by a multiple sensor-neural network approach.

3. Codon usage divergence of homologous vertebrate genes and codon usage clock.

4. Comparison of the patterns of codon usage and bias between Brugia, Echinococcus, Onchocerca and Schistosoma species.

5. EumicrobeDBLite: a lightweight genomic resource and analytic platform for draft oomycete genomes.

6. The current status and portability of our sequence handling software.

7. The codon Adaptation Index--a measure of directional synonymous codon usage bias, and its potential applications.

8. DNA sequence of the lactose operon: the lacA gene and the transcriptional termination region.

9. Codon usage patterns suggest independent evolution of two catabolic operons on toluene-degradative plasmid TOL pWW0 of Pseudomonas putida.

10. Codon usage and gene expression.