CAIcal: a combined set of tools to assess codon usage adaptation (Q36909725)

17 August 2017

CAIcal: a combined set of tools to assess codon usage adaptation (English)

1 reference

17 August 2017

Santiago Garcia-Vallvé

object named as

Santiago Garcia-Vallve

series ordinal

3

0 references

author name string

Pere Puigbò

series ordinal

1

1 reference

17 August 2017

Ignacio G Bravo

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2

1 reference

17 August 2017

16 September 2008

1 reference

17 August 2017

1 reference

17 August 2017

3

1 reference

17 August 2017

38

1 reference

The CAI Analyser Package: inferring gene expressivity from raw genomic data

17 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2553769

E-CAI: a novel server to estimate an expected value of Codon Adaptation Index (eCAI).

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2553769

Different papillomaviruses have different repertoires of transcription factor binding sites: convergence and divergence in the upstream regulatory region

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2553769

Papillomaviruses: different genes have different histories.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2553769

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2553769

The papillomavirus life cycle

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2553769

The viral E4 protein is required for the completion of the cottontail rabbit papillomavirus productive cycle in vivo

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2553769

HGT-DB: a database of putative horizontally transferred genes in prokaryotic complete genomes

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2553769

EMBOSS: the European Molecular Biology Open Software Suite

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2553769

Codon usage tabulated from international DNA sequence databases: status for the year 2000

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2553769

Codon catalog usage and the genome hypothesis

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2553769

Codon usage in bacteria: correlation with gene expressivity

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2553769

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2553769

Human papillomavirus type 1 produces redundant as well as polycistronic mRNAs in plantar warts

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2553769

The 'effective number of codons' used in a gene

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2553769

An improved implementation of codon adaptation index

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2553769

HEG-DB: a database of predicted highly expressed genes in prokaryotic complete genomes under translational selection

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2553769

OPTIMIZER: a web server for optimizing the codon usage of DNA sequences

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2553769

Multiple evolutionary mechanisms drive papillomavirus diversification

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2553769

An environmental signature for 323 microbial genomes based on codon adaptation indices

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2553769

Patterns of nucleotide difference in overlapping and non-overlapping reading frames of papillomavirus genomes

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2553769

Predicted highly expressed genes in Nocardia farcinica and the implication for its primary metabolism and nocardial virulence

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2553769

Predicted highly expressed genes in the genomes of Streptomyces coelicolor and Streptomyces avermitilis and the implications for their metabolism

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2553769

Codon usage bias and A+T content variation in human papillomavirus genomes

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2553769

Codon adaptation index as a measure of dominating codon bias.

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2553769

Horizontal gene transfer in glycosyl hydrolases inferred from codon usage in Escherichia coli and Bacillus subtilis

4 September 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/18796141

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1186/1745-6150-3-38

1 reference

Dimensions Publication ID

17 August 2017

0 references

1 reference

17 August 2017

PubMed publication ID

18796141

1 reference