{"id":"W4393180770","doi":"10.3390/applmicrobiol4020042","title":"In Silico Prophage Analysis of Halobacterium salinarum ATCC 33170","year":2024,"lang":"en","type":"article","venue":"Applied Microbiology","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":3,"is_retracted":false,"has_abstract":true,"ca_institutions":"Brock University; National Research Council Canada","funders":"National Research Council Canada","keywords":"Halobacterium salinarum; In silico; Prophage; Computational biology; Biology; Genetics; Gene; Archaea; Escherichia coli","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":[0.0003685491,0.0008396731,0.0007601858,0.001314265,0.0002695925,0.0007654772,0.0003965958,0.0005023101,0.001124484],"category_scores_gemma":[0.0007190717,0.0002396238,0.001114365,0.001299491,0.0001087602,0.0001972943,0.0003872749,0.0004336871,0.0009013265],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0002154938,"about_ca_system_score_gemma":0.0004644769,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001915234,"about_ca_topic_score_gemma":0.001328078,"domain_scores_codex":[0.9996533,0.00004225191,0.00004159527,0.00007391929,0.0001326728,0.00005623473],"domain_scores_gemma":[0.9996499,0.0001461733,0.00005586304,0.00002573711,0.00008089236,0.00004137003],"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":[0.0006883273,0.0001768929,0.009500507,0.0004754813,0.0000648157,0.0009195106,0.0002061047,0.00248813,0.9766778,0.0001020423,0.0001961592,0.008504099],"study_design_scores_gemma":[0.0001407638,0.002803636,0.1557224,0.0001923282,0.0006045368,0.002629688,0.001356187,0.03703266,0.7823871,0.0005670225,0.01642125,0.000142387],"study_design_candidate":"simulation_or_modeling","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9869514,0.0008282181,0.003385352,0.000096171,0.00002583401,0.0001299906,0.007194425,0.0001650119,0.001223658],"genre_scores_gemma":[0.9157934,0.001768374,0.03105081,0.0001336081,0.0000218505,0.000245092,0.04858044,0.0001958845,0.002210654],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.001915234,"threshold_uncertainty_score":0.003808141,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.00493439182750484,"score_gpt":0.225117951273367,"score_spread":0.2201835594458622,"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."}}