{"id":"W2098816661","doi":"10.1101/gr.081778.108","title":"Multiple whole-genome alignments without a reference organism","year":2009,"lang":"en","type":"article","venue":"Genome Research","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":78,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Toronto","funders":"Basic Energy Sciences; National Institute of General Medical Sciences; Natural Sciences and Engineering Research Council of Canada; Office of Science; National Institutes of Health; U.S. Department of Energy","keywords":"Genome; Biology; Reference genome; Comparative genomics; Whole genome sequencing; Computational biology; Genomics; Genetics; Multiple sequence alignment; Genome project; Sequence alignment; Gene","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":[0.001195444,0.001991637,0.001762571,0.002899636,0.001523664,0.001816784,0.00176181,0.001671757,0.02317299],"category_scores_gemma":[0.004488329,0.001155338,0.001846099,0.003992462,0.0003116683,0.0020536,0.001937463,0.002131266,0.01143102],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000583892,"about_ca_system_score_gemma":0.001086879,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001006363,"about_ca_topic_score_gemma":0.002530779,"domain_scores_codex":[0.9987525,0.000193845,0.0001738411,0.0006030014,0.0001992262,0.0000776349],"domain_scores_gemma":[0.9988204,0.0002956402,0.0001963916,0.0004152601,0.0002205177,0.00005181504],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.002190528,0.0004410805,0.007323076,0.004292476,0.001821962,0.001841153,0.0009781683,0.008799599,0.6209081,0.01755805,0.06867941,0.2651663],"study_design_scores_gemma":[0.0003667394,0.0006025489,0.02915241,0.0005007086,0.001549022,0.004552519,0.0007886603,0.07094098,0.3309224,0.03370522,0.526632,0.0002868612],"study_design_candidate":"simulation_or_modeling","study_design_consensus":null,"genre_codex":"methods","genre_gemma":"methods","genre_scores_codex":[0.1052633,0.004075728,0.7100352,0.000606128,0.001088217,0.0006351988,0.1056653,0.05009534,0.0225356],"genre_scores_gemma":[0.1097514,0.001543071,0.6870679,0.0002388118,0.00008119374,0.0005788983,0.1831201,0.008419814,0.009198816],"genre_candidate":"methods","genre_consensus":"methods","teacher_disagreement_score":0.02317299,"threshold_uncertainty_score":0.07752144,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.06292475297984731,"score_gpt":0.3379405761540632,"score_spread":0.2750158231742159,"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."}}