{"id":"W2117641249","doi":"10.1093/molbev/msq102","title":"The Influence of Anticodon-Codon Interactions and Modified Bases on Codon Usage Bias in Bacteria","year":2010,"lang":"en","type":"article","venue":"Molecular Biology and Evolution","topic":"RNA and protein synthesis mechanisms","field":"Biochemistry, Genetics and Molecular Biology","cited_by":78,"is_retracted":false,"has_abstract":true,"ca_institutions":"McMaster University","funders":"","keywords":"Wobble base pair; Transfer RNA; Codon usage bias; Biology; Genetics; Gene; Translation (biology); Genetic code; Genome; Speed wobble; Start codon; Ribosome; Base pair; RNA; Messenger RNA","routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":false},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.000328629,0.0001098503,0.0001137891,0.00005383514,0.000105312,0.00001226369,0.00008851483,0.0001687797,0.000003033605],"category_scores_gemma":[0.0003015015,0.00008315692,0.00003089949,0.00005490434,0.0001968423,0.00000546985,0.00006099488,0.0001212643,0.000001350714],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000004500177,"about_ca_system_score_gemma":0.00002054849,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00009164297,"about_ca_topic_score_gemma":0.0002341281,"domain_scores_codex":[0.9992329,0.0001680655,0.0001721357,0.0002361161,0.00003872529,0.0001520028],"domain_scores_gemma":[0.9995632,0.00006395827,0.00008297877,0.0002174263,0.00003660652,0.00003579961],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.000144313,0.00002524884,0.007955927,0.000006526895,0.00001326288,0.000001058319,0.00001360808,0.00003103985,0.984356,0.005714424,0.000006765522,0.00173184],"study_design_scores_gemma":[0.0003522908,0.0003635358,0.1329179,0.00002865125,0.00001215942,0.00002167447,0.00002528278,0.0001381651,0.8618547,0.002730633,0.001415028,0.0001400294],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9972275,0.0002817363,0.001877477,0.0001837387,0.0001276974,0.0001517597,0.00001025112,0.000004784747,0.0001350704],"genre_scores_gemma":[0.9992687,0.0002171875,0.0003196762,0.00008647673,0.00002675203,0.0000204353,0.00002014641,0.000007424445,0.00003319072],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.1249619,"threshold_uncertainty_score":0.3391041,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01212622839146649,"score_gpt":0.2692455015707776,"score_spread":0.2571192731793111,"validation_status":"score_only:v0-immature-baseline","note":"Baseline scores from an immature model (maturity gate not passed). Scores rank; they never assert a category."}}