get_fop {cubar}

Fraction of optimal codons (Fop)

Description

get_fop calculates the fraction of optimal codons (Fop) of each CDS.

Usage

get_fop(seqs, codon_table = get_codon_table())

Arguments

seqs

CDS sequences of all protein-coding genes. One for each gene.

codon_table

a table of genetic code derived from 'get_codon_table' or 'create_codon_table'.

Value

a named vector of fop values.

References

Ikemura T. 1981. 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. J Mol Biol 151:389-409.

Examples

# estimate Fop of yeast genes
fop <- get_fop(yeast_cds)
head(fop)
hist(fop)