{"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":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0005833454,0.0000933374,0.0001052912,0.0001488046,0.0002476787,0.00002304251,0.0002261554,0.00006553838,0.0002268545],"category_scores_gemma":[0.0001031815,0.0001024577,0.00005924333,0.0002719063,0.0000699099,0.000003696259,0.000372497,0.0001917774,0.00001510873],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001453228,"about_ca_system_score_gemma":0.0001240995,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00003836424,"about_ca_topic_score_gemma":0.000003335258,"domain_scores_codex":[0.9984067,0.0001334627,0.0002043096,0.0003015468,0.0007028144,0.0002511308],"domain_scores_gemma":[0.999414,0.00005169674,0.00003204199,0.0002207916,0.000188494,0.00009303734],"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":[0.0001956458,0.0001314822,0.001759813,0.00007407171,0.00003781779,0.00001144902,0.0008699783,0.04385985,0.9411862,0.002026764,0.007175438,0.002671467],"study_design_scores_gemma":[0.00101132,0.002470023,0.01368654,0.00008660773,0.00001528393,0.0002084318,0.01705055,0.03200214,0.8826948,0.0004794202,0.04972,0.0005749143],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.8003222,0.0004648754,0.1968553,0.0002458236,0.0002563746,0.0003170742,0.00004456971,0.00002021799,0.001473637],"genre_scores_gemma":[0.9873157,0.000004023977,0.01184947,0.00004594852,0.0001698702,0.0001265639,0.00006025227,0.00001998871,0.0004081478],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.1869936,"threshold_uncertainty_score":0.4178105,"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."}}