{"id":"W2901247228","doi":"10.3390/v10110637","title":"Base-By-Base Version 3: New Comparative Tools for Large Virus Genomes","year":2018,"lang":"en","type":"article","venue":"Viruses","topic":"Plant Virus Research Studies","field":"Agricultural and Biological Sciences","cited_by":26,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Victoria","funders":"Natural Sciences and Engineering Research Council of Canada","keywords":"Sequence (biology); Genome; Computational biology; Base (topology); Computer science; Biology; Base pair; Oligonucleotide; Multiple sequence alignment; Sequence alignment; Java; Gene; Sequence analysis; Genetics; Consensus sequence; Base sequence; Peptide sequence; Programming language","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":[0.007878235,0.00309282,0.002625169,0.005407951,0.001511639,0.003099925,0.00538657,0.002044355,0.03954099],"category_scores_gemma":[0.01198645,0.002899006,0.002551921,0.003458218,0.0007642159,0.004552227,0.003775295,0.004685063,0.0170569],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0007893753,"about_ca_system_score_gemma":0.001942582,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001273694,"about_ca_topic_score_gemma":0.001861975,"domain_scores_codex":[0.9972547,0.0008437111,0.0004420458,0.0004073653,0.0008244194,0.0002277641],"domain_scores_gemma":[0.9953364,0.003000936,0.0003911277,0.0005925203,0.0004079707,0.0002712174],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"not_applicable","study_design_gemma":"not_applicable","study_design_scores_codex":[0.003669191,0.0006062482,0.003785855,0.00672332,0.001373465,0.002293458,0.002576716,0.004665643,0.1380263,0.01921998,0.4466068,0.370453],"study_design_scores_gemma":[0.0009932792,0.0004057082,0.00606513,0.001246618,0.0004100402,0.004063297,0.0003558654,0.03936732,0.05691716,0.02430887,0.8650376,0.000829014],"study_design_candidate":"not_applicable","study_design_consensus":"not_applicable","genre_codex":"methods","genre_gemma":"software","genre_scores_codex":[0.007360147,0.00233773,0.5683689,0.000322955,0.001191421,0.0006876715,0.0314324,0.3831372,0.005161449],"genre_scores_gemma":[0.01643336,0.00120801,0.8619894,0.0003253464,0.0001991585,0.001774781,0.03810522,0.0767215,0.003243263],"genre_candidate":"software","genre_consensus":null,"teacher_disagreement_score":0.03954099,"threshold_uncertainty_score":0.1322777,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.1681599408599732,"score_gpt":0.3383143105184616,"score_spread":0.1701543696584884,"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."}}