{"id":"W4376871556","doi":"10.1093/nar/gkad382","title":"PHASTEST: faster than PHASTER, better than PHAST","year":2023,"lang":"en","type":"article","venue":"Nucleic Acids Research","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":589,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Alberta","funders":"Canadian Institutes of Health Research; Genome Alberta; Genome Canada","keywords":"Prophage; Genome; Bacterial genome size; Annotation; Biology; GenBank; Visualization; Computational biology; Genome project; Genetics; Computer science; Gene; Data mining; Bacteriophage","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":[0.0008172333,0.0002233332,0.0002038908,0.000195922,0.0003310904,0.00009612211,0.0005600545,0.0001753002,0.0001298742],"category_scores_gemma":[0.00009322214,0.0002018952,0.0001317664,0.0004579042,0.0002968384,0.000001860724,0.0007801153,0.0002703464,0.0006971072],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00002035226,"about_ca_system_score_gemma":0.00006997033,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00003191978,"about_ca_topic_score_gemma":0.00004394951,"domain_scores_codex":[0.997566,0.0001669971,0.0002384093,0.0006291628,0.0004979655,0.0009014346],"domain_scores_gemma":[0.9988476,0.00005106631,0.00003867529,0.0006749869,0.0002144382,0.0001732338],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"not_applicable","study_design_scores_codex":[0.0001018632,0.00008457071,0.02786785,0.00002565434,0.0001245908,0.00001802912,0.0003829689,0.000009404332,0.9329376,0.0000470729,0.02193655,0.01646388],"study_design_scores_gemma":[0.002936419,0.001735154,0.1122585,0.00004941734,0.00002811581,0.00004384317,0.001675209,0.0003937108,0.1793529,0.001042801,0.699659,0.000824803],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9885338,0.0004508053,0.00005695356,0.001173948,0.0002545118,0.0002996414,0.00008279115,0.00001665193,0.009130918],"genre_scores_gemma":[0.9908185,0.0003600461,0.000239839,0.0002116494,0.000828958,0.00007788668,0.00008378574,0.00006726079,0.007312064],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.7535846,"threshold_uncertainty_score":0.8960135,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.05710669052715073,"score_gpt":0.3415770212536993,"score_spread":0.2844703307265485,"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."}}