cubar (version 1.2.0)

est_trna_weight: Estimate tRNA weights for TAI calculation

Description

est_trna_weight calculates tRNA weights for each codon based on tRNA availability and codon-anticodon pairing efficiency. These weights are used in tRNA Adaptation Index (TAI) calculations and reflect how well each codon is supported by the cellular tRNA pool.

Usage

est_trna_weight(
  trna_level,
  codon_table = get_codon_table(),
  domain = "Eukarya",
  s = NULL
)

Value

A data.table containing comprehensive tRNA weight information with columns:

• aa_code: Single-letter amino acid code

• amino_acid: Three-letter amino acid abbreviation

• codon: Codon sequence

• subfam: Codon subfamily identifier

• anticodon: Corresponding anticodon sequence

• trna_id: tRNA identifier (amino_acid-anticodon)

• ac_level: tRNA abundance level

• W: Absolute adaptiveness value

• w: Relative adaptiveness (normalized weight for TAI)

Arguments

trna_level

A named numeric vector of tRNA expression levels or gene copy numbers. Names should be in the format "AminoAcid-Anticodon" (e.g., "Ala-GCA"). Each value represents the abundance of that tRNA species.

codon_table

A codon table defining the genetic code, derived from get_codon_table() or create_codon_table().

domain

Character string specifying the taxonomic domain: "Eukarya" (default), "Bacteria", or "Archaea". This determines the codon-anticodon pairing rules and selection penalties. Specify either "domain" or "s".

s

A named list of selection penalties for non-Watson-Crick pairings. If provided, overrides the default domain-specific penalties. Specify either "domain" or "s".

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.

Sabi R, Tuller T. 2014. Modelling the efficiency of codon-tRNA interactions based on codon usage bias. DNA Res 21:511-526.

Examples

# Calculate tRNA weights for yeast using gene copy numbers
yeast_trna_w <- est_trna_weight(yeast_trna_gcn)
head(yeast_trna_w)

# View the weight distribution
hist(yeast_trna_w$w, main = "Distribution of tRNA weights")