{"id":"W4295241395","doi":"10.1016/j.biosystems.2022.104771","title":"Genome-scale prediction of bacterial promoters","year":2022,"lang":"en","type":"article","venue":"Biosystems","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":6,"is_retracted":false,"has_abstract":false,"ca_institutions":"Dalhousie University","funders":"Natural Sciences and Engineering Research Council of Canada","keywords":"Promoter; Biology; Genome; Genetics; Computational biology; Gene; RNA polymerase; DNA; Consensus sequence; Transcription (linguistics); DNA sequencing; RNA; Gene expression; Base sequence","routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":false},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0002714661,0.0006359185,0.0006043193,0.0007324496,0.0003878353,0.0006623666,0.0003952587,0.0005448143,0.001204598],"category_scores_gemma":[0.0008295022,0.0003088276,0.0005930205,0.0006756085,0.0002113023,0.0003341193,0.0003364897,0.0009133727,0.001447394],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0005019088,"about_ca_system_score_gemma":0.0008719945,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.002066275,"about_ca_topic_score_gemma":0.003253889,"domain_scores_codex":[0.9998831,0.00002547828,0.000005092785,0.00003631084,0.00003096308,0.00001897378],"domain_scores_gemma":[0.9996793,0.0001560626,0.0000271626,0.00003403911,0.00006295788,0.00004054985],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.001979428,0.0005585615,0.0283203,0.0009232768,0.0001379353,0.001093226,0.0002092932,0.1246785,0.7225481,0.007999617,0.005385773,0.1061661],"study_design_scores_gemma":[0.0001650513,0.0003981147,0.02270241,0.00008386964,0.0001421461,0.0004685785,0.0002694913,0.7427131,0.2057505,0.0122577,0.0150055,0.000043632],"study_design_candidate":"simulation_or_modeling","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.8209116,0.002332122,0.1556533,0.0004660984,0.00008666973,0.0001234362,0.01117112,0.004690796,0.004564738],"genre_scores_gemma":[0.8871059,0.0007535901,0.08632874,0.00007252792,0.00002410756,0.00006345169,0.02395927,0.0003133259,0.001379063],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.002066275,"threshold_uncertainty_score":0.004108429,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.00943816777362904,"score_gpt":0.1927187262435288,"score_spread":0.1832805584698997,"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."}}