{"id":"W4412033208","doi":"10.1093/bioadv/vbaf162","title":"Volcano: a pipeline to characterize long terminal repeat-retrotransposons families in plants","year":2024,"lang":"en","type":"article","venue":"Bioinformatics Advances","topic":"Chromosomal and Genetic Variations","field":"Agricultural and Biological Sciences","cited_by":0,"is_retracted":false,"has_abstract":true,"ca_institutions":"Innovation, Science and Economic Development Canada","funders":"Beijing Academy of Agricultural and Forestry Sciences; Chinese Academy of Sciences","keywords":"Retrotransposon; Long terminal repeat; Genome; Biology; Pipeline (software); Computational biology; Genetics; Computer science; Gene; Transposable element","routes":{"ca_aff":true,"ca_fund":false,"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":[0.001156914,0.002123051,0.0007707818,0.002437786,0.001075795,0.001166526,0.001353377,0.0008379339,0.008970122],"category_scores_gemma":[0.002655415,0.0008623814,0.002281394,0.001289331,0.0004645258,0.001549237,0.001241969,0.001120104,0.003888466],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0008950198,"about_ca_system_score_gemma":0.001332601,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.005251505,"about_ca_topic_score_gemma":0.00596562,"domain_scores_codex":[0.9995438,0.00005022044,0.00003506975,0.0002181185,0.000095144,0.00005772003],"domain_scores_gemma":[0.9993306,0.0002957913,0.00009514676,0.00008388251,0.0001099464,0.0000845959],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"design_other","study_design_gemma":"not_applicable","study_design_scores_codex":[0.003428706,0.0004564187,0.05324189,0.003493943,0.001153385,0.001288121,0.003028689,0.02432789,0.3092259,0.007513368,0.2153193,0.3775224],"study_design_scores_gemma":[0.0008470833,0.0007456836,0.06326465,0.0002648445,0.0005107027,0.001337501,0.000978556,0.5492567,0.1563741,0.01897542,0.2069723,0.000472353],"study_design_candidate":"not_applicable","study_design_consensus":null,"genre_codex":"software","genre_gemma":"software","genre_scores_codex":[0.06630554,0.0008558254,0.3672434,0.0005301284,0.0001505448,0.0007142241,0.0821604,0.4782313,0.00380866],"genre_scores_gemma":[0.1995642,0.0005344482,0.591001,0.0005183282,0.00009820774,0.001127577,0.1773177,0.02588169,0.003956691],"genre_candidate":"software","genre_consensus":"software","teacher_disagreement_score":0.008970122,"threshold_uncertainty_score":0.03000802,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01568206321207271,"score_gpt":0.2369625222065186,"score_spread":0.2212804589944458,"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."}}