CodonO: codon usage bias analysis within and across genomes. (Q30362021)

15 October 2017

CodonO: codon usage bias analysis within and across genomes. (English)

1 reference

15 October 2017

1 reference

Michael C Angellotti

1

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15 October 2017

Shafquat B Bhuiyan

series ordinal

2

1 reference

15 October 2017

Guorong Chen

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3

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15 October 2017

Xiu-Feng Wan

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4

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15 October 2017

language of work or name

English

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publication date

30 May 2007

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15 October 2017

Nucleic Acids Research

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15 October 2017

35

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15 October 2017

W132-6

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15 October 2017

Web Server issue

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JCat: a novel tool to adapt codon usage of a target gene to its potential expression host

15 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933134

Quantitative relationship between synonymous codon usage bias and GC composition across unicellular genomes

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933134

The relationship between synonymous codon usage and protein structure in Escherichia coli and Homo sapiens.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933134

Synonymous codon usage is subject to selection in thermophilic bacteria

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933134

Correlations between Shine-Dalgarno sequences and gene features such as predicted expression levels and operon structures

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933134

Shannon information theoretic computation of synonymous codon usage biases in coding regions of human and mouse genomes

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933134

A simple model based on mutation and selection explains trends in codon and amino-acid usage and GC composition within and across genomes

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933134

What drives codon choices in human genes?

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933134

Hydrophobicity, expressivity and aromaticity are the major trends of amino-acid usage in 999 Escherichia coli chromosome-encoded genes

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933134

3 June 2018

Codon selection in yeast

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933134

Codon usage in bacteria: correlation with gene expressivity

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933134

The codon preference plot: graphic analysis of protein coding sequences and prediction of gene expression.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933134

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933134

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933134

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933134

Synonymous codon usage in Bacillus subtilis reflects both translational selection and mutational biases

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933134

Compositional constraints and genome evolution

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1933134

The base composition of the genes is correlated with the secondary structures of the encoded proteins

3 June 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/17537810

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Codon distribution in vertebrate genes may be used to predict gene length

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/17537810

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1093/NAR/GKM392

1 reference

journals/nar/AngellottiBCW07

15 October 2017

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

15 October 2017

1 reference