{"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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.001389527,0.001128215,0.001634568,0.001045669,0.001528688,0.001725307,0.001277351,0.001099592,0.006155112],"category_scores_gemma":[0.002276313,0.0009535658,0.001698169,0.001146903,0.0007804694,0.0006727589,0.0009778203,0.00325597,0.005599361],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.001106336,"about_ca_system_score_gemma":0.002896923,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.005655093,"about_ca_topic_score_gemma":0.02008667,"domain_scores_codex":[0.9989108,0.00009368837,0.00007527541,0.0004495432,0.0003050062,0.0001657808],"domain_scores_gemma":[0.9985473,0.0002935725,0.0001042446,0.0003239822,0.0005219175,0.0002089318],"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":[0.0002689581,0.00006945548,0.0008906744,0.0004023756,0.00007532623,0.0001098606,0.0002542592,0.0009287818,0.979162,0.001755518,0.004200198,0.01188275],"study_design_scores_gemma":[0.0001719756,0.0002699076,0.01341951,0.0001676625,0.0002413254,0.0003860105,0.0002222839,0.01658213,0.8385699,0.003450432,0.126359,0.0001600033],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"methods","genre_gemma":"methods","genre_scores_codex":[0.2615997,0.003359938,0.5325451,0.0007583416,0.00145924,0.002200639,0.1583573,0.01109283,0.02862679],"genre_scores_gemma":[0.2141839,0.001739371,0.5191067,0.002606221,0.0001567439,0.001715331,0.2247923,0.007072225,0.02862716],"genre_candidate":"methods","genre_consensus":"methods","teacher_disagreement_score":0.006155112,"threshold_uncertainty_score":0.0205909,"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."}}