{"id":"W3194505801","doi":"10.1101/2021.08.20.457124","title":"Spacer2PAM: A computational framework for identification of functional PAM sequences for endogenous CRISPR systems","year":2021,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"CRISPR and Genetic Engineering","field":"Biochemistry, Genetics and Molecular Biology","cited_by":0,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"Joint Genome Institute; Suncor Energy Incorporated; U.S. Department of Energy; David and Lucile Packard Foundation; National Science Foundation","keywords":"CRISPR; Trans-activating crRNA; Computational biology; CRISPR interference; Biology; Genome editing; Computer science; Genetics; Gene","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":[0.001275789,0.001617022,0.001549808,0.001042787,0.0008335245,0.001472223,0.002685298,0.001504548,0.01039464],"category_scores_gemma":[0.003120731,0.0008467477,0.001557881,0.0006477673,0.000620621,0.001024373,0.001541015,0.001474983,0.001200374],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0009988967,"about_ca_system_score_gemma":0.002115773,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.005041755,"about_ca_topic_score_gemma":0.009482546,"domain_scores_codex":[0.9996754,0.0001296052,0.00001823988,0.00006478946,0.0000767364,0.00003521809],"domain_scores_gemma":[0.99896,0.00079779,0.00005042995,0.00004519119,0.0000757322,0.00007092053],"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":[0.0003019692,0.0001960784,0.002126836,0.0006314055,0.0002116057,0.0003440941,0.00008710342,0.9259071,0.003508717,0.02861452,0.007517458,0.0305531],"study_design_scores_gemma":[0.00004340916,0.00001917251,0.00004465179,0.00001279367,0.0000121216,0.00001396904,0.00001071737,0.9928085,0.0005010906,0.004791346,0.001734885,0.000007356351],"study_design_candidate":"simulation_or_modeling","study_design_consensus":"simulation_or_modeling","genre_codex":"methods","genre_gemma":"methods","genre_scores_codex":[0.03304859,0.0004874091,0.9336874,0.0004201244,0.0001120647,0.0002756771,0.002532601,0.02297949,0.006456622],"genre_scores_gemma":[0.2503922,0.000464051,0.7388088,0.0002997093,0.00007202428,0.001508967,0.003872767,0.002189246,0.002392244],"genre_candidate":"methods","genre_consensus":"methods","teacher_disagreement_score":0.01039464,"threshold_uncertainty_score":0.03477353,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02318256366303384,"score_gpt":0.2729775222914282,"score_spread":0.2497949586283943,"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."}}