Codon usage database

GCO CodonFrequency tormat only. For more organisms, cnecK out tne Codon usage Database... 

TmPrime includes a codon optimizing feature. It implements global codon optimization that replaces each codon based on the organism-specific codon frequencies using the organism-specific codon data in the Codon Usage Database (http//www.kazusa. 

Guigo R. (1999) DNA composition, codon usage and exon prediction. In Genetics Databases. Academic Press, 54-80. 

ANACONDA is a software package specially developed for the study of genes primary structure. It reads ORFeomes downloaded from public databases in FASTA format and uses a set of statistical and visualization methods to reveal information about codon context, codon usage, and nucleotide repeats within ORFs. The general features of ANACONDA are described below ... 

Parameters the reference values of relative synonymous codon usage (RSCU) are necessary for the calculation of the codon adaptation index (CAI) (19). This data must be introduced manually. In the current version, the ANACONDA database includes RSCU values for Candida albicans, Saccharomyces cerevisiae, and Escherichia coli. 

In this section, we describe the main tools of ANACONDA which are divided into four main parts, namely (1) uploading and validation of DNA sequence data into the local database, (2) building ORFeome maps for two-codon context bias, (3) visualization and analysis of the two-codon context biases in individual sequences, and (4) comparison of the codon biases across multiple ORFeomes. Also, and taking advantage of the fact that ANACONDA interprets DNA sequences as sequences of trinucleotides (codons), several tools regarding codon usage analysis have been implemented, as explained next. 

Codon usage from GenBank (CUTG) Eukaryotic promoter database (EPD) Functional molecular immunology ... 

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