{"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":"codex-gemma-dda1882f352a","candidate_categories":["insufficient_payload"],"consensus_categories":[],"category_scores_codex":[0.0001874303,0.0001542655,0.000214524,0.00001478767,0.0005254057,0.0001226494,0.0002674178,0.00005814938,0.001118024],"category_scores_gemma":[0.0001641209,0.00005817209,0.00007594171,0.0002036938,0.00009920346,0.0003196296,0.0001336547,0.00006879012,0.0007740887],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00003140747,"about_ca_system_score_gemma":0.00001896377,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0005022101,"about_ca_topic_score_gemma":0.001787603,"domain_scores_codex":[0.9988201,0.00006055654,0.000146384,0.0003013282,0.0002298992,0.0004416843],"domain_scores_gemma":[0.9988219,0.0008092474,0.00005715219,0.00005781062,0.00009953591,0.0001543341],"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":[0.0001496289,0.00006086137,0.0002596453,0.000002611796,0.00002177629,0.000001071256,0.00008327032,1.300917e-7,0.6563483,0.00009472013,0.3379586,0.00501931],"study_design_scores_gemma":[0.0002307026,0.0004472159,0.001510844,0.00000964744,0.000006952318,4.25376e-7,0.0002342712,0.00002345271,0.3383759,0.0001107014,0.6589209,0.0001290018],"study_design_candidate":"not_applicable","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9878907,0.00144542,0.0000353796,0.0007995318,0.0001378347,0.0004761881,0.008228476,0.0001072073,0.0008792119],"genre_scores_gemma":[0.9922618,0.0007102245,0.0003981241,0.002893656,0.001239376,0.00006783701,0.0005288285,0.000002503451,0.001897631],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.3209623,"threshold_uncertainty_score":0.9997951,"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."}}