{"id":"W2125810118","doi":"10.1093/bioinformatics/btm224","title":"RankMotif++: a motif-search algorithm that accounts for relative ranks of K-mers in binding transcription factors","year":2007,"lang":"en","type":"article","venue":"Bioinformatics","topic":"Genomics and Chromatin Dynamics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":67,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Toronto","funders":"Natural Sciences and Engineering Research Council of Canada; Ontario Genomics; Ontario Genomics Institute; Genome Canada","keywords":"Motif (music); DNA binding site; Computational biology; Computer science; Algorithm; Data mining; Biology; Genetics; 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":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0006063162,0.0001546375,0.0001916964,0.0001562828,0.00005568731,0.00001899113,0.0001733209,0.0002204081,0.000004401062],"category_scores_gemma":[0.00004104462,0.0001461807,0.0001254873,0.0001239516,0.00005862363,0.00001982089,0.00003746775,0.0001026507,0.000002399315],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00004937262,"about_ca_system_score_gemma":0.00005676147,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00002131049,"about_ca_topic_score_gemma":0.00004243804,"domain_scores_codex":[0.9989172,0.00001374422,0.000451333,0.0001320062,0.0001693028,0.0003163634],"domain_scores_gemma":[0.9994755,0.00003546409,0.0001571276,0.0001916412,0.00007986287,0.00006034272],"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":[0.0007753845,0.0005653608,0.04841971,0.001493318,0.0005802874,0.000004819028,0.02263591,0.002162886,0.7890289,0.001048633,0.0004005267,0.1328842],"study_design_scores_gemma":[0.00983486,0.00145898,0.05931707,0.0002651582,0.0001386195,0.00002408254,0.02709976,0.2031202,0.6930381,0.0005037948,0.003772823,0.001426556],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.8300479,0.0000590404,0.1686796,0.00001110139,0.0001521451,0.000393923,0.0001867036,0.000005943192,0.0004636092],"genre_scores_gemma":[0.9583421,0.00009790799,0.04093239,0.00002112811,0.00003051321,0.000006023207,0.0004005717,0.00002024906,0.0001491543],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.2009573,"threshold_uncertainty_score":0.5961074,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02064250354701683,"score_gpt":0.2618901333386715,"score_spread":0.2412476297916547,"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."}}