Warning: Undefined array key "mm" in /www/wwwroot/www.ai-bt.com/si.php on line 10 Deprecated: trim(): Passing null to parameter #1 ($string) of type string is deprecated in /www/wwwroot/www.ai-bt.com/si.php on line 10 Codon preference and primary sequence structure in protein-coding regions.

Literature DB >> 2706404

Codon preference and primary sequence structure in protein-coding regions.

Abstract

The stochastic complexity of a data base of 365 protein-coding regions is analysed. When the primary sequence is modeled as a spatially homogeneous Markov source, the fit to observed codon preference is very poor. The situation improves substantially when a non-homogeneous model is used. Some implications for the estimation of species phylogeny and substitution rates are discussed.

Mesh：

Substances：

Year: 1989 PMID： 2706404 DOI： 10.1007/BF02458838

Source DB: PubMed Journal: Bull Math Biol ISSN： 0092-8240 Impact factor: 1.758

28 in total

1. A measure of the similarity of sets of sequences not requiring sequence alignment.

Authors: B E Blaisdell
Journal: Proc Natl Acad Sci U S A Date: 1986-07 Impact factor: 11.205

2. Codon usage tabulated from the GenBank genetic sequence data.

Authors: T Maruyama; T Gojobori; S Aota; T Ikemura
Journal: Nucleic Acids Res Date: 1986 Impact factor: 16.971

3. On the distribution of the nucleotides in seven completely sequenced DNAs.

Authors: C Fuchs
Journal: Gene Date: 1980-09 Impact factor: 3.688

4. Contextual constraints on synonymous codon choice.

Authors: D J Lipman; W J Wilbur
Journal: J Mol Biol Date: 1983-01-25 Impact factor: 5.469

5. Markov analysis of viral DNA/RNA sequences.

Authors: P W Garden
Journal: J Theor Biol Date: 1980-02-21 Impact factor: 2.691

6. Significance of the information content of DNA in mutations and evolution.

Authors: J Subba Rao; C P Geevan; G Subba Rao
Journal: J Theor Biol Date: 1982-06-21 Impact factor: 2.691

Review 7. Preferential codon usage in prokaryotic genes: the optimal codon-anticodon interaction energy and the selective codon usage in efficiently expressed genes.

Authors: H Grosjean; W Fiers
Journal: Gene Date: 1982-06 Impact factor: 3.688

6. The Caenorhabditis elegans gene unc-89, required fpr muscle M-line assembly, encodes a giant modular protein composed of Ig and signal transduction domains.

Authors: G M Benian; T L Tinley; X Tang; M Borodovsky
Journal: J Cell Biol Date: 1996-03 Impact factor: 10.539

6 in total

Codon preference and primary sequence structure in protein-coding regions.

1. A measure of the similarity of sets of sequences not requiring sequence alignment.

2. Codon usage tabulated from the GenBank genetic sequence data.

3. On the distribution of the nucleotides in seven completely sequenced DNAs.

4. Contextual constraints on synonymous codon choice.

5. Markov analysis of viral DNA/RNA sequences.

6. Significance of the information content of DNA in mutations and evolution.

Review 7. Preferential codon usage in prokaryotic genes: the optimal codon-anticodon interaction energy and the selective codon usage in efficiently expressed genes.

8. The carB gene of Escherichia coli: a duplicated gene coding for the large subunit of carbamoyl-phosphate synthetase.

9. Markedly unbiased codon usage in Bacillus subtilis.

1. A hidden Markov model that finds genes in E. coli DNA.

2. Uniform Accuracy of the Maximum Likelihood Estimates for Probabilistic Models of Biological Sequences.

3. Intrinsic and extrinsic approaches for detecting genes in a bacterial genome.

4. Detection of new genes in a bacterial genome using Markov models for three gene classes.

5. On the representability of complete genomes by multiple competing finite-context (Markov) models.

6. The Caenorhabditis elegans gene unc-89, required fpr muscle M-line assembly, encodes a giant modular protein composed of Ig and signal transduction domains.