{"id":"W3210646027","doi":"10.4236/aim.2021.1110039","title":"Minimal Secondary Structure Formation on mRNAs with a Shine-Dalgarno Sequence for Chromosomal Genes in &amp;lt;i&amp;gt;Rhodobacter sphaeroides&amp;lt;/i&amp;gt;","year":2021,"lang":"en","type":"article","venue":"Advances in Microbiology","topic":"RNA and protein synthesis mechanisms","field":"Biochemistry, Genetics and Molecular Biology","cited_by":0,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Calgary","funders":"Directorate for Biological Sciences","keywords":"Biology; Genetics; Rhodobacter sphaeroides; Gene; Shine-Dalgarno sequence; Start codon; Protein biosynthesis; Untranslated region; Open reading frame; Messenger RNA; Ribosomal binding site; Plasmid; Coding region; Replicon; Five prime untranslated region; Protein secondary structure; RNA; Translational efficiency; GC-content; Ribosome; Translation (biology); Peptide sequence; Biochemistry; Genome","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":["metaepi_narrow"],"consensus_categories":[],"category_scores_codex":[0.0002898065,0.0004742917,0.0005364935,0.0001307403,0.0001193589,0.00004144815,0.0003992339,0.0005421976,0.0003275029],"category_scores_gemma":[0.0002027087,0.0004178768,0.000135108,0.0002200384,0.0002038471,0.00006102097,0.0001448928,0.0002726293,0.00002866783],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00008328306,"about_ca_system_score_gemma":0.0001866555,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000007451681,"about_ca_topic_score_gemma":0.007344073,"domain_scores_codex":[0.9973816,0.0002875358,0.0006023924,0.0009257786,0.00009322432,0.0007095049],"domain_scores_gemma":[0.9986827,0.000128885,0.0002937109,0.0006483433,0.0001590699,0.00008724699],"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":[0.0008089768,0.00007300733,0.0006664324,0.0001133108,0.00004320903,0.00001344209,0.0001520214,0.0002686859,0.9807859,0.0001426744,0.0002185982,0.01671376],"study_design_scores_gemma":[0.00115757,0.0003102091,0.0001816667,0.0001147069,0.00001908722,0.0003839896,0.00002608986,0.000002618036,0.6222696,0.0005200243,0.374588,0.000426425],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9803557,0.01016652,0.007351613,0.0002416537,0.0004154338,0.0006342853,0.0005181842,0.00002338465,0.0002932486],"genre_scores_gemma":[0.9117632,0.001767327,0.07955942,0.0009651658,0.0003608402,0.000214593,0.004331716,0.00007737713,0.0009603658],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.3743694,"threshold_uncertainty_score":0.9998273,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01459432919555911,"score_gpt":0.2655581874278132,"score_spread":0.2509638582322541,"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."}}