{"id":"W2143861586","doi":"10.1186/1759-8753-4-28","title":"A pipeline of programs for collecting and analyzing group II intron retroelement sequences from GenBank","year":2013,"lang":"en","type":"article","venue":"Mobile DNA","topic":"RNA and protein synthesis mechanisms","field":"Biochemistry, Genetics and Molecular Biology","cited_by":13,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Calgary","funders":"Canadian Institutes of Health Research","keywords":"Intron; Group II intron; GenBank; Group I catalytic intron; Biology; Genetics; Genome; Computational biology; Phylogenetic tree; RNA splicing; Gene; RNA","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":[0.000185033,0.0001003592,0.0001489926,0.00002192449,0.00009725877,0.00002304662,0.00009100202,0.00007883986,0.00004497086],"category_scores_gemma":[0.00004469524,0.00008679298,0.00005571829,0.00005003643,0.00003486807,0.000004197495,0.00007256863,0.0000267981,8.184131e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00000803515,"about_ca_system_score_gemma":0.00001484887,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0002040202,"about_ca_topic_score_gemma":0.00004655468,"domain_scores_codex":[0.9992821,0.00003322059,0.0002030724,0.0002479062,0.00006702157,0.0001666513],"domain_scores_gemma":[0.9996125,0.00001822131,0.0001091594,0.0001560438,0.00006187218,0.00004226959],"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":[0.00002760807,0.00003646026,0.0009148636,0.00002017904,0.00003527073,1.433559e-7,0.00006821419,0.000003437474,0.9296591,0.00001376766,0.000400305,0.06882069],"study_design_scores_gemma":[0.0003826242,0.001059544,0.0001412363,0.0000304375,0.00002674448,0.000001033532,0.0002604067,0.0003899455,0.9877309,0.0006536604,0.009194381,0.0001291241],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9919392,0.001314653,0.005627634,0.00004672019,0.0000523973,0.0008960536,0.0000187843,0.000008194047,0.00009633762],"genre_scores_gemma":[0.9881352,0.00008361085,0.01049711,0.00003093719,0.0001480295,0.000689726,0.0001045986,0.00001279064,0.0002979671],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.06869157,"threshold_uncertainty_score":0.3539315,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01211639478589936,"score_gpt":0.2421951376997121,"score_spread":0.2300787429138128,"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."}}