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Estimate tRNA weights for TAI calculation

Source: R/codon_weight.R
est_trna_weight.Rd

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
)

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".

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)

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)
#>    aa_code amino_acid  codon subfam anticodon trna_id ac_level       W
#>     <char>     <char> <char> <char>    <char>  <char>  <table>   <num>
#> 1:       F        Phe    TTT Phe_TT       AAA Phe-AAA        0  2.1390
#> 2:       F        Phe    TTC Phe_TT       GAA Phe-GAA       10 10.0000
#> 3:       L        Leu    TTA Leu_TT       TAA Leu-TAA        7  7.0000
#> 4:       L        Leu    TTG Leu_TT       CAA Leu-CAA       10 12.5935
#> 5:       S        Ser    TCT Ser_TC       AGA Ser-AGA       11 11.0000
#> 6:       S        Ser    TCC Ser_TC       GGA Ser-GGA        0  5.8751
#>            w
#>        <num>
#> 1: 0.1289059
#> 2: 0.6026456
#> 3: 0.4218519
#> 4: 0.7589418
#> 5: 0.6629102
#> 6: 0.3540603

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