{"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":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0001278212,0.0001516199,0.0003128704,0.0001748916,0.00002022598,0.000007871561,0.0001542193,0.0001681455,0.00003721907],"category_scores_gemma":[0.000006101048,0.0001367731,0.0001330121,0.0003449732,0.0001261517,3.89195e-7,0.0001537203,0.00006946249,0.00001818448],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001258126,"about_ca_system_score_gemma":0.00004245169,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00002886108,"about_ca_topic_score_gemma":0.0001235384,"domain_scores_codex":[0.9990301,0.00002731247,0.0002711928,0.0004118047,0.00001932212,0.0002403084],"domain_scores_gemma":[0.999626,0.00001766315,0.00004433125,0.0002621817,0.00002454032,0.00002522995],"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":[0.00004492134,0.00003715845,0.001367744,0.0000286313,0.0006810667,0.000004845299,0.0001045377,0.00008825763,0.9957401,0.0007298538,0.0007066614,0.0004662789],"study_design_scores_gemma":[0.0003350648,0.0001736188,0.007637018,0.000006957593,0.0003258462,0.00001380419,0.00007754142,0.00003484504,0.9072149,0.0001929578,0.08371957,0.0002678249],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9951481,0.003094133,0.00009660943,0.0001140121,0.0001963644,0.0001646566,0.0001456429,0.000004619525,0.001035882],"genre_scores_gemma":[0.9986324,0.000225857,0.0002769135,0.0001948136,0.00007527406,0.00003180526,0.0002691506,0.00001544625,0.0002783634],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.08852509,"threshold_uncertainty_score":0.5577447,"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."}}