{"id":"W4213036952","doi":"10.1093/nar/gkac142","title":"Spacer2PAM: A computational framework to guide experimental determination of functional CRISPR-Cas system PAM sequences","year":2022,"lang":"en","type":"article","venue":"Nucleic Acids Research","topic":"CRISPR and Genetic Engineering","field":"Biochemistry, Genetics and Molecular Biology","cited_by":18,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"Joint Genome Institute; National Science Foundation Graduate Research Fellowship Program; Suncor Energy Incorporated; U.S. Department of Energy; David and Lucile Packard Foundation; National Science Foundation","keywords":"CRISPR; Computational biology; Biology; Trans-activating crRNA; Effector; CRISPR interference; Genome editing; Synthetic biology; Genetics; Gene; Cell biology","routes":{"ca_aff":false,"ca_fund":true,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":true},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.001654478,0.001609929,0.001557572,0.0008006247,0.0007738578,0.001397352,0.00279847,0.001372766,0.01075286],"category_scores_gemma":[0.003867276,0.000827846,0.001373164,0.0005391584,0.0006309646,0.0009121756,0.001493565,0.001980372,0.001601667],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000955243,"about_ca_system_score_gemma":0.002732753,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.004726334,"about_ca_topic_score_gemma":0.008627012,"domain_scores_codex":[0.9996307,0.0001244184,0.00002295914,0.00008268092,0.00009981778,0.00003938327],"domain_scores_gemma":[0.9988159,0.0008848983,0.00005491608,0.00005988915,0.0001086601,0.00007575956],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"simulation_or_modeling","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.0006583298,0.0003204659,0.00442075,0.001349822,0.0004142486,0.0006595985,0.0002015503,0.8222451,0.0115559,0.04474216,0.03126438,0.08216771],"study_design_scores_gemma":[0.00008585928,0.00003872805,0.0001290204,0.00002429603,0.00002593412,0.0000312101,0.00001868877,0.9821031,0.002333081,0.008569592,0.00662237,0.0000182419],"study_design_candidate":"simulation_or_modeling","study_design_consensus":"simulation_or_modeling","genre_codex":"methods","genre_gemma":"methods","genre_scores_codex":[0.02139947,0.0003765933,0.9303941,0.0004374343,0.0001337593,0.0002667323,0.00345046,0.03682711,0.006714423],"genre_scores_gemma":[0.1677617,0.000546194,0.8149725,0.0004276723,0.00005699405,0.001770757,0.006781608,0.004825881,0.002856678],"genre_candidate":"methods","genre_consensus":"methods","teacher_disagreement_score":0.01075286,"threshold_uncertainty_score":0.03597188,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.03436691995092781,"score_gpt":0.3970631307690581,"score_spread":0.3626962108181302,"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."}}