{"id":"W1483946786","doi":"10.1186/s40168-015-0086-5","title":"Strong spurious transcription likely contributes to DNA insert bias in typical metagenomic clone libraries","year":2015,"lang":"en","type":"article","venue":"Microbiome","topic":"RNA and protein synthesis mechanisms","field":"Biochemistry, Genetics and Molecular Biology","cited_by":24,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Waterloo","funders":"Natural Sciences and Engineering Research Council of Canada; Canadian Institutes of Health Research; University of Waterloo; Compute Canada; Genome Canada","keywords":"Fosmid; Cosmid; Biology; Metagenomics; Library; Genetics; Genomic library; DNA; Computational biology; Genome; Transcription (linguistics); Gene; 16S ribosomal RNA","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":[],"consensus_categories":[],"category_scores_codex":[0.0003003724,0.0001693756,0.0002227752,0.0001244948,0.00003686917,0.00007996049,0.000219551,0.0001918004,0.00002266193],"category_scores_gemma":[0.00006522588,0.0001621539,0.00007609122,0.0001589686,0.00004612851,0.00001153256,0.000073347,0.00006614527,0.0001005232],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00003529383,"about_ca_system_score_gemma":0.00009714389,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00004393221,"about_ca_topic_score_gemma":0.00007238686,"domain_scores_codex":[0.998954,0.000111319,0.0002498874,0.000326653,0.00006385727,0.0002942894],"domain_scores_gemma":[0.9995347,0.000009584589,0.0000426571,0.0002526024,0.00004047175,0.0001199724],"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":[0.0004233673,0.0000605664,0.0002218068,0.00000851724,0.00003590761,0.000005938589,0.0001207226,0.00001216809,0.9959828,0.0002937996,0.001578781,0.001255665],"study_design_scores_gemma":[0.0007692503,0.0002425899,0.001058397,0.00001677171,0.00001432862,0.00001002348,0.00008059409,0.000003175752,0.9091751,0.0002695266,0.08817376,0.000186488],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9907374,0.002404714,0.005270342,0.0007977365,0.0002460578,0.0003431978,0.00004427051,0.00002076016,0.0001355438],"genre_scores_gemma":[0.9961551,0.00002869749,0.002329669,0.0005400364,0.00009856179,0.00003642458,0.0001262292,0.00002630831,0.000658964],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.08680767,"threshold_uncertainty_score":0.6612445,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.04222491878896383,"score_gpt":0.2496453572024908,"score_spread":0.207420438413527,"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."}}