codon usage analysis

Question

[sayna_shahdparvar]

hi, I do codon usage analysing,but I have some problems in finding the softwares which I need,first of all I want to access NC and GC3s ,then I need NC-pot to draw the plot of NC & GC3s, ...I will be thankfull if help me in this way.

Answer 1

[natasha.sernova]

See these posts:

Generating Codon Usage

How To Perform A Codon Usage Analysis

Codon Usage Database

Open Reading Frame And Codons

Amino Acid Content Statistical Test

refseq NC id list download

Finding Frequent To Rare Codon From The Codon Table Of Human

http://www.bioinformatics.org/sms2/codon_usage.html

and these papers:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2174420/

ACUA: A software tool for automated codon usage analysis (from 2007)

http://www.ncbi.nlm.nih.gov/pubmed/26019240

GC3-biased gene domains in mammalian genomes. (from 2015)

What are your genomes?

Codon usage is slightly different in bacteria, in archaea, in plants and plastids, viruses and bacteriophages,

in mitochondrial genomes, etc?

Most genomes can be found in NCBI, but you have to choose some narrow group.