ecolik12: E. coli K-12 codon bias and tRNA numbers

In mariodosreis/tai: The tRNA adaptation index

E. coli K-12 codon bias and tRNA numbers

Description

A list with elements trna, a vector of length 64 of tRNA gene copy numbers in the Escherichia coli K-12 genome, w, a data frame with some codon bias statistics for 49 E. coli K-12 coding genes, and m, a 49 by 61 matrix of codon frequencies for the 49 genes in question.

Usage

ecolik12

Format

An object of class list of length 3.

Author(s)

Mario dos Reis

Examples

# 87 tRNA genes in the E. coli K-12 genome:
sum(ecolik12$trna)

# Two copies are isoacceptors for Phe, with anticodon GAA (codon TTC)
ecolik12$trna[2]

# ecolik12$w, a data frame with codon bias statistics
names(ecolik12$w)

# Effective number of codons vs. gene length (in codons)
plot(ecolik12$w$Nc, ecolik12$w$L_aa, xlab="Nc", ylab="Gene length")

mariodosreis/tai documentation built on June 9, 2022, 7:37 p.m.