{"id":"W3014602217","doi":"10.1038/s41596-020-0301-0","title":"Full-length sequencing of circular DNA viruses and extrachromosomal circular DNA using CIDER-Seq","year":2020,"lang":"en","type":"article","venue":"Nature Protocols","topic":"Bacteriophages and microbial interactions","field":"Environmental Science","cited_by":87,"is_retracted":false,"has_abstract":false,"ca_institutions":"University of Alberta","funders":"Fonds De La Recherche Scientifique - FNRS; Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung","keywords":"Extrachromosomal DNA; DNA sequencing; Rolling circle replication; DNA; Sequencing by ligation; Biology; Computational biology; Genome; In vitro recombination; Multiple displacement amplification; Sequence analysis; DNA nanoball sequencing; Genetics; Polymerase chain reaction; Plasmid; Molecular cloning; DNA extraction; DNA polymerase; Complementary DNA; Gene; Genomic library; Base sequence","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":"codex-gemma-dda1882f352a","candidate_categories":["insufficient_payload"],"consensus_categories":[],"category_scores_codex":[0.0001190695,0.0002032196,0.0002582022,0.00002835347,0.0001453896,0.00006781131,0.0002207414,0.0002551328,0.0009421394],"category_scores_gemma":[0.00007759806,0.0001941069,0.000102689,0.0002301003,0.0001499576,0.0004198388,0.0001950493,0.0005280386,0.00003606815],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001548171,"about_ca_system_score_gemma":0.00003717413,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0001099936,"about_ca_topic_score_gemma":0.00001754129,"domain_scores_codex":[0.9987054,0.000067609,0.000304731,0.0004293018,0.000224807,0.0002681323],"domain_scores_gemma":[0.9993885,0.00002894396,0.000178114,0.0002312344,0.00002160502,0.0001515625],"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":[0.00004013104,0.00003677326,0.001055287,0.0001128503,0.00002339832,0.00003129523,0.000381131,0.00008950504,0.9972076,0.00002155801,0.0001022653,0.0008981369],"study_design_scores_gemma":[0.0008054237,0.0002990066,0.01033,0.0002577564,0.00006302277,0.0002346141,0.0001758523,0.00153342,0.9557519,0.0001305034,0.0299421,0.0004764323],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9806069,0.00007967868,0.0007452727,0.0002178214,0.00006003969,0.01762084,0.00003343364,0.00005728066,0.0005787995],"genre_scores_gemma":[0.9935118,0.000002451076,0.003042522,0.0009725904,0.0001175296,0.002305896,0.00000385623,0.00003005444,0.00001327403],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.0414558,"threshold_uncertainty_score":0.9999712,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.04034942459925112,"score_gpt":0.3056424790291684,"score_spread":0.2652930544299172,"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."}}