Modal codon usage: assessing the typical codon usage of a genome (Q33730013)

29 July 2017

title

Modal codon usage: assessing the typical codon usage of a genome (English)

1 reference

29 July 2017

James J Davis

1

1 reference

29 July 2017

Gary J Olsen

series ordinal

2

1 reference

29 July 2017

publication date

17 December 2009

1 reference

Molecular Biology and Evolution

29 July 2017

published in

1 reference

29 July 2017

volume

27

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29 July 2017

issue

4

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29 July 2017

page(s)

800-810

1 reference

Thermoanaerobacter pseudethanolicus sp. nov., a thermophilic heterotrophic anaerobe from Yellowstone National Park

29 July 2017

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2839124

Database resources of the National Center for Biotechnology Information

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2839124

Mutational and selective pressures on codon and amino acid usage in Buchnera, endosymbiotic bacteria of aphids.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2839124

Isolation and characterization of metal-reducing thermoanaerobacter strains from deep subsurface environments of the Piceance Basin, Colorado

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2839124

A new type IV secretion system promotes conjugal transfer in Agrobacterium tumefaciens

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2839124

Genome Sequence of the Plant Pathogen and Biotechnology Agent Agrobacterium tumefaciens C58

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2839124

The genome of the natural genetic engineer Agrobacterium tumefaciens C58

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2839124

Predicted highly expressed genes of diverse prokaryotic genomes

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2839124

Codon usage and lateral gene transfer in Bacillus subtilis

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2839124

Proteome composition and codon usage in spirochaetes: species-specific and DNA strand-specific mutational biases

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2839124

Petrotoga mobilis sp. nov., from a North Sea oil-production well

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2839124

Replicational and transcriptional selection on codon usage in Borrelia burgdorferi

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2839124

GCUA: general codon usage analysis

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2839124

The complete genome sequence of the gram-positive bacterium Bacillus subtilis

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2839124

Thermosipho melanesiensis sp. nov., a new thermophilic anaerobic bacterium belonging to the order Thermotogales, isolated from deep-sea hydrothermal vents in the southwestern Pacific Ocean

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2839124

Amelioration of bacterial genomes: rates of change and exchange

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2839124

Linear DNA of Borrelia species and antigenic variation

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2839124

Codon catalog usage and the genome hypothesis

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2839124

Codon usage in bacteria: correlation with gene expressivity

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2839124

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2839124

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2839124

Codon frequencies in 119 individual genes confirm consistent choices of degenerate bases according to genome type.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2839124

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2839124

Evidence for horizontal gene transfer in Escherichia coli speciation

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2839124

Low-passage-associated proteins of Borrelia burgdorferi B31: characterization and molecular cloning of OspD, a surface-exposed, plasmid-encoded lipoprotein.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2839124

Transfer of virulence in vivo and in vitro in Agrobacterium

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2839124

Genome sequence of the endocellular obligate symbiont of tsetse flies, Wigglesworthia glossinidia

28 July 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSP281

A bacterial genome in flux: the twelve linear and nine circular extrachromosomal DNAs in an infectious isolate of the Lyme disease spirochete Borrelia burgdorferi

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSP281

Genomic sequence of a Lyme disease spirochaete, Borrelia burgdorferi

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSP281

Gene expression level influences amino acid usage, but not codon usage, in the tsetse fly endosymbiont Wigglesworthia.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSP281

Role of outer surface protein D in the Borrelia burgdorferi life cycle

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSP281

A Simplex Method for Function Minimization

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSP281

The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSP281

Complete nucleotide sequence of the freshwater unicellular cyanobacterium Synechococcus elongatus PCC 6301 chromosome: gene content and organization

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSP281

Synonymous codon usage in Pseudomonas aeruginosa PA01.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2839124

Codon catalog usage is a genome strategy modulated for gene expressivity

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2839124

Ti plasmids of Agrobacterium as conjugative plasmids

30 October 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSP281

Physical mapping of an origin of bidirectional replication at the centre of the Borrelia burgdorferi linear chromosome

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/20018979

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/20018979

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1093/MOLBEV/MSP281

1 reference

29 July 2017

1 reference

29 July 2017

1 reference