{"id":"W2111327312","doi":"10.1534/genetics.104.037887","title":"A Unified Model of Codon Reassignment in Alternative Genetic Codes","year":2005,"lang":"en","type":"article","venue":"Genetics","topic":"RNA and protein synthesis mechanisms","field":"Biochemistry, Genetics and Molecular Biology","cited_by":54,"is_retracted":false,"has_abstract":true,"ca_institutions":"McMaster University","funders":"","keywords":"Transfer RNA; Genetic code; Biology; Genetics; Genome; Selection (genetic algorithm); Mutation; Function (biology); Codon usage bias; Computational biology; Gene; RNA; Computer science","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":[0.0001335961,0.0001279188,0.0001480628,0.00004792044,0.0000189215,0.000006643876,0.0001996142,0.0001135333,0.00001576694],"category_scores_gemma":[0.00002131355,0.0001281863,0.00005098603,0.00005148635,0.00004626813,0.000001370695,0.00007741317,0.00004246823,0.000006341577],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0000175325,"about_ca_system_score_gemma":0.00005677107,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00001153465,"about_ca_topic_score_gemma":0.0001077354,"domain_scores_codex":[0.9990979,0.00006097247,0.0002571042,0.0002430244,0.0001473863,0.0001935406],"domain_scores_gemma":[0.9994871,0.000008531581,0.00009282454,0.0003102731,0.00004719194,0.00005407701],"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":[0.00005037526,0.0000680548,0.0005495343,0.000009535877,0.00001960242,0.00000118255,0.0000851997,0.05344558,0.934396,0.000206676,0.0000816076,0.01108664],"study_design_scores_gemma":[0.0004192944,0.000169349,0.0006198341,0.00001623589,0.00001104508,0.000003402556,0.00003143609,0.01666989,0.9794832,0.0008868177,0.001539774,0.0001497521],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9623994,0.0009744607,0.03539697,0.00007628527,0.00003936394,0.0002121172,0.00002460288,0.000004541372,0.0008722328],"genre_scores_gemma":[0.956171,0.0007085176,0.0425146,0.0001086079,0.00009200763,0.00002555528,0.00001246056,0.00001928913,0.0003480068],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.04508716,"threshold_uncertainty_score":0.5227286,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.0210548729574947,"score_gpt":0.2505766397134398,"score_spread":0.2295217667559451,"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."}}