{"id":"W1931155698","doi":"10.1139/w11-095","title":"Analysis of synonymous codon usage in<i>Shigella flexneri</i>2a strain 301 and other<i>Shigella</i>and<i>Escherichia coli</i>strains","year":2011,"lang":"en","type":"article","venue":"Canadian Journal of Microbiology","topic":"RNA and protein synthesis mechanisms","field":"Biochemistry, Genetics and Molecular Biology","cited_by":2,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"","keywords":"Codon usage bias; Genetics; Biology; Synonymous substitution; Shigella flexneri; Shigella; Genome; Gene; Strain (injury); Start codon; Silent mutation; Escherichia coli; Mutation; Base sequence","routes":{"ca_aff":false,"ca_fund":false,"ca_venue":true,"about_ca":false,"invisible_to_affiliation_only":true},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0001277987,0.0002572766,0.0003509505,0.0006426625,0.0002077642,0.0002385627,0.0001183178,0.0001971149,0.0006618044],"category_scores_gemma":[0.0004365289,0.00009329669,0.0003127723,0.0005996238,0.0001454798,0.0001144158,0.0001090808,0.0001957617,0.0002093834],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001981721,"about_ca_system_score_gemma":0.0001635559,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001126652,"about_ca_topic_score_gemma":0.002362482,"domain_scores_codex":[0.9998666,0.00002533421,0.0000170447,0.00003355956,0.00003663232,0.00002086974],"domain_scores_gemma":[0.9996154,0.00009843908,0.000133647,0.00003258866,0.00006878653,0.00005101802],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","study_design_scores_codex":[0.000213396,0.00001851609,0.01159428,0.00006903269,0.00002513033,0.0001158506,0.0000809242,0.0001039808,0.9854475,0.00004320005,0.00001669397,0.002271408],"study_design_scores_gemma":[0.00001850837,0.0007180804,0.5938091,0.00002649202,0.0001516515,0.002498546,0.0004475213,0.002259227,0.3975192,0.0002139744,0.002296236,0.00004149521],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9987368,0.000187256,0.0005448984,0.00000788129,0.000002938632,0.000005601493,0.0002797873,0.000008149596,0.0002267179],"genre_scores_gemma":[0.996291,0.0002011878,0.001700853,0.0000221175,0.000005029687,0.00001428833,0.001528332,0.0000139333,0.0002232325],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.001126652,"threshold_uncertainty_score":0.002240181,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01675516401578083,"score_gpt":0.2130449060232383,"score_spread":0.1962897420074575,"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."}}