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)
)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)
#> aa_code amino_acid codon subfam anticodon ac_level W w
#> <char> <char> <char> <char> <char> <table> <num> <num>
#> 1: F Phe TTT Phe_TT AAA 0 2.1390 0.12890590
#> 2: F Phe TTC Phe_TT GAA 10 10.0000 0.60264561
#> 3: L Leu TTA Leu_TT TAA 7 7.0000 0.42185193
#> 4: L Leu TTG Leu_TT CAA 10 12.5935 0.75894175
#> 5: S Ser TCT Ser_TC AGA 11 11.0000 0.66291018
#> 6: S Ser TCC Ser_TC GGA 0 5.8751 0.35406032
#> 7: S Ser TCA Ser_TC TGA 3 4.0175 0.24211288
#> 8: S Ser TCG Ser_TC CGA 1 2.1115 0.12724862
#> 9: Y Tyr TAT Tyr_TA ATA 0 NA 0.25960862
#> 10: Y Tyr TAC Tyr_TA GTA 8 8.0000 0.48211649
#> 11: C Cys TGT Cys_TG ACA 0 NA 0.25960862
#> 12: C Cys TGC Cys_TG GCA 4 4.0000 0.24105825
#> 13: W Trp TGG Trp_TG CCA 6 6.0000 0.36158737
#> 14: L Leu CTT Leu_CT AAG 0 0.2139 0.01289059
#> 15: L Leu CTC Leu_CT GAG 1 1.0000 0.06026456
#> 16: L Leu CTA Leu_CT TAG 3 3.0000 0.18079368
#> 17: L Leu CTG Leu_CT CAG 0 1.1115 0.06698406
#> 18: P Pro CCT Pro_CC AGG 2 2.0000 0.12052912
#> 19: P Pro CCC Pro_CC GGG 0 1.0682 0.06437460
#> 20: P Pro CCA Pro_CC TGG 10 10.1850 0.61379456
#> 21: P Pro CCG Pro_CC CGG 0 3.7050 0.22328020
#> 22: H His CAT His_CA ATG 0 1.4973 0.09023413
#> 23: H His CAC His_CA GTG 7 7.0000 0.42185193
#> 24: Q Gln CAA Gln_CA TTG 9 9.0000 0.54238105
#> 25: Q Gln CAG Gln_CA CTG 1 4.3345 0.26121674
#> 26: R Arg CGT Arg_CG ACG 6 6.0000 0.36158737
#> 27: R Arg CGC Arg_CG GCG 0 3.2046 0.19312381
#> 28: R Arg CGA Arg_CG TCG 0 0.5550 0.03344683
#> 29: R Arg CGG Arg_CG CCG 1 1.0000 0.06026456
#> 30: I Ile ATT Ile_AT AAT 13 13.0000 0.78343930
#> 31: I Ile ATC Ile_AT GAT 0 6.9433 0.41843493
#> 32: I Ile ATA Ile_AT TAT 2 3.2025 0.19299726
#> 33: M Met ATG Met_AT CAT 10 10.0000 0.60264561
#> 34: T Thr ACT Thr_AC AGT 11 11.0000 0.66291018
#> 35: T Thr ACC Thr_AC GGT 0 5.8751 0.35406032
#> 36: T Thr ACA Thr_AC TGT 4 5.0175 0.30237744
#> 37: T Thr ACG Thr_AC CGT 1 2.4820 0.14957664
#> 38: N Asn AAT Asn_AA ATT 0 2.1390 0.12890590
#> 39: N Asn AAC Asn_AA GTT 10 10.0000 0.60264561
#> 40: K Lys AAA Lys_AA TTT 7 7.0000 0.42185193
#> 41: K Lys AAG Lys_AA CTT 14 16.5935 1.00000000
#> 42: S Ser AGT Ser_AG ACT 0 0.4278 0.02578118
#> 43: S Ser AGC Ser_AG GCT 2 2.0000 0.12052912
#> 44: R Arg AGA Arg_AG TCT 11 11.0000 0.66291018
#> 45: R Arg AGG Arg_AG CCT 1 5.0755 0.30587278
#> 46: V Val GTT Val_GT AAC 14 14.0000 0.84370386
#> 47: V Val GTC Val_GT GAC 0 7.4774 0.45062223
#> 48: V Val GTA Val_GT TAC 2 3.2950 0.19857173
#> 49: V Val GTG Val_GT CAC 2 2.7410 0.16518516
#> 50: A Ala GCT Ala_GC AGC 11 11.0000 0.66291018
#> 51: A Ala GCC Ala_GC GGC 0 5.8751 0.35406032
#> 52: A Ala GCA Ala_GC TGC 5 6.0175 0.36264200
#> 53: A Ala GCG Ala_GC CGC 0 1.8525 0.11164010
#> 54: D Asp GAT Asp_GA ATC 0 3.4224 0.20624944
#> 55: D Asp GAC Asp_GA GTC 16 16.0000 0.96423298
#> 56: E Glu GAA Glu_GA TTC 14 14.0000 0.84370386
#> 57: E Glu GAG Glu_GA CTC 2 7.1870 0.43312140
#> 58: G Gly GGT Gly_GG ACC 0 3.4224 0.20624944
#> 59: G Gly GGC Gly_GG GCC 16 16.0000 0.96423298
#> 60: G Gly GGA Gly_GG TCC 3 3.0000 0.18079368
#> 61: G Gly GGG Gly_GG CCC 2 3.1115 0.18751318
#> aa_code amino_acid codon subfam anticodon ac_level W w