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Literature DB >> 6364041

Measurements of the effects that coding for a protein has on a DNA sequence and their use for finding genes.

Abstract

Protein genes can be found either by searching the DNA sequence for signals such as ribosome binding sites or by looking for the effects that coding for a protein has on the coding sequence. This paper describes how these coding effects can be measured and used to detect protein coding regions.

Mesh：

Substances：
Codon
Proteins
DNA
Myosins

Year: 1984 PMID： 6364041 PMCID： PMC321070 DOI： 10.1093/nar/12.1part2.551

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

7 in total

1. Nucleotide sequence of bacteriophage lambda DNA.

Authors: F Sanger; A R Coulson; G F Hong; D F Hill; G B Petersen
Journal: J Mol Biol Date: 1982-12-25 Impact factor: 5.469

2. 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

3. Molecular analysis of the unc-54 myosin heavy-chain gene of Caenorhabditis elegans.

Authors: A R MacLeod; J Karn; S Brenner
Journal: Nature Date: 1981-06-04 Impact factor: 49.962

4. Nucleotide sequence of the gene ompA coding the outer membrane protein II of Escherichia coli K-12.

Authors: E Beck; E Bremer
Journal: Nucleic Acids Res Date: 1980-07-11 Impact factor: 16.971

5. 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

6. Recognition of protein coding regions in DNA sequences.

Authors: J W Fickett
Journal: Nucleic Acids Res Date: 1982-09-11 Impact factor: 16.971

7. 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

7 in total

97 in total

1. Archaeal adaptation to higher temperatures revealed by genomic sequence of Thermoplasma volcanium.

Authors: T Kawashima; N Amano; H Koike; S Makino; S Higuchi; Y Kawashima-Ohya; K Watanabe; M Yamazaki; K Kanehori; T Kawamoto; T Nunoshiba; Y Yamamoto; H Aramaki; K Makino; M Suzuki
Journal: Proc Natl Acad Sci U S A Date: 2000-12-19 Impact factor: 11.205

2. GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions.

Authors: J Besemer; A Lomsadze; M Borodovsky
Journal: Nucleic Acids Res Date: 2001-06-15 Impact factor: 16.971

Measurements of the effects that coding for a protein has on a DNA sequence and their use for finding genes.

1. Nucleotide sequence of bacteriophage lambda DNA.

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

3. Molecular analysis of the unc-54 myosin heavy-chain gene of Caenorhabditis elegans.

4. Nucleotide sequence of the gene ompA coding the outer membrane protein II of Escherichia coli K-12.

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

6. Recognition of protein coding regions in DNA sequences.

7. 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.

1. Archaeal adaptation to higher temperatures revealed by genomic sequence of Thermoplasma volcanium.

2. GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions.

3. Mining Bacillus subtilis chromosome heterogeneities using hidden Markov models.

4. ZCURVE: a new system for recognizing protein-coding genes in bacterial and archaeal genomes.

5. Induction of a Streptomyces cacaoi beta-lactamase gene cloned in S. lividans.

Review 6. Assessment of protein coding measures.

7. Computer prediction of the exon-intron structure of mammalian pre-mRNAs.

8. Suppression of a frameshift mutation in the recE gene of Escherichia coli K-12 occurs by gene fusion.

9. Accurate mapping of the Escherichia coli pepD gene by sequence analysis of its 5' flanking region.

10. Nonrandom utilization of codon pairs in Escherichia coli.