est_trna_weight {cubar}

Estimate tRNA weight w

Description

est_trna_weight compute the tRNA weight per codon for TAI calculation. This weight reflects relative tRNA availability for each codon.

Usage

est_trna_weight(
  trna_level,
  codon_table = get_codon_table(),
  s = list(WC = 0, IU = 0, IC = 0.4659, IA = 0.9075, GU = 0.7861, UG = 0.6295)
)

Arguments

trna_level

named vector of tRNA level (or gene copy numbers), one value for each anticodon. vector names are anticodons.

codon_table

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

s

list of non-Waston-Crick pairing panelty.

Value

data.table of tRNA expression information.

References

dos Reis M, Savva R, Wernisch L. 2004. Solving the riddle of codon usage preferences: a test for translational selection. Nucleic Acids Res 32:5036-5044.

Examples

# estimate codon tRNA weight for yeasts
est_trna_weight(yeast_trna_gcn)