{"id":"W1984672010","doi":"10.1371/journal.pone.0068712","title":"Optimized Position Weight Matrices in Prediction of Novel Putative Binding Sites for Transcription Factors in the Drosophila melanogaster Genome","year":2013,"lang":"en","type":"article","venue":"PLoS ONE","topic":"Genomics and Chromatin Dynamics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":2,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Ottawa","funders":"Natural Sciences and Engineering Research Council of Canada","keywords":"Drosophila melanogaster; Transcription factor; Computational biology; DNA binding site; Promoter; Biology; Binding site; Genome; Genetics; Gene; Gene expression","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":[0.000584111,0.000548353,0.0003893304,0.00118771,0.0001573764,0.0003522952,0.000409235,0.0003055245,0.0008652782],"category_scores_gemma":[0.002546895,0.0002369701,0.0004121405,0.001059253,0.0001096774,0.0004204524,0.0002319762,0.0004180631,0.0003843587],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001988873,"about_ca_system_score_gemma":0.0005132259,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001568531,"about_ca_topic_score_gemma":0.002526205,"domain_scores_codex":[0.999803,0.00005601709,0.00001430393,0.00004731976,0.00006425289,0.00001517523],"domain_scores_gemma":[0.9996144,0.0002192175,0.00004793202,0.00002401651,0.00007776856,0.00001661682],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"design_other","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.00110834,0.0003000648,0.01618283,0.0008446007,0.0001892725,0.0003718662,0.0002571414,0.2992359,0.2348043,0.004581474,0.001855598,0.4402685],"study_design_scores_gemma":[0.0001023168,0.000232055,0.00684936,0.00003571936,0.00009242042,0.0002054816,0.00009352598,0.9378315,0.04715405,0.004539346,0.002825823,0.0000383809],"study_design_candidate":"simulation_or_modeling","study_design_consensus":null,"genre_codex":"methods","genre_gemma":"empirical","genre_scores_codex":[0.4127409,0.001156842,0.5815148,0.00008300496,0.00002870107,0.0001029566,0.001238852,0.002219593,0.0009143224],"genre_scores_gemma":[0.4884939,0.0005527995,0.5070006,0.00002398219,0.00001256675,0.0001135596,0.00292674,0.0002523233,0.0006236054],"genre_candidate":"empirical","genre_consensus":null,"teacher_disagreement_score":0.001568531,"threshold_uncertainty_score":0.003118873,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02556441317473665,"score_gpt":0.2131501494713789,"score_spread":0.1875857362966423,"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."}}