{"id":"W1793459287","doi":"10.1093/bioinformatics/btv420","title":"CEMAsuite: open source degenerate PCR primer design","year":2015,"lang":"en","type":"article","venue":"Bioinformatics","topic":"Molecular Biology Techniques and Applications","field":"Biochemistry, Genetics and Molecular Biology","cited_by":16,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"Division of Chemical, Bioengineering, Environmental, and Transport Systems; Egg Farmers of Canada; Louisiana State University; National Science Foundation","keywords":"Primer (cosmetics); Suite; Computer science; Source code; Computational biology; Sequence (biology); Coding (social sciences); Multiple sequence alignment; Sequence alignment; Biology; Genetics; Programming language; Gene; Peptide sequence; Mathematics; Statistics","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":[0.0003916969,0.0001504815,0.0001291494,0.0000304591,0.00008675206,0.00007647564,0.0005480683,0.0001814169,0.00001127745],"category_scores_gemma":[0.0000680546,0.0001311182,0.00004785932,0.0001003642,0.00007031711,0.000008674944,0.0004446935,0.0000684703,0.00009341099],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001482561,"about_ca_system_score_gemma":0.0001617126,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00001530199,"about_ca_topic_score_gemma":0.000003048017,"domain_scores_codex":[0.9991888,0.00004621973,0.0002674889,0.0001705779,0.0000983573,0.0002285464],"domain_scores_gemma":[0.9990727,0.000005500533,0.0001196483,0.0005234089,0.000122332,0.0001564464],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"not_applicable","study_design_gemma":"not_applicable","study_design_scores_codex":[0.0002385014,0.0002908313,0.001234885,0.00004630575,0.0002103503,0.000004155514,0.0005246238,0.001561588,0.3089684,0.005384481,0.6369715,0.04456436],"study_design_scores_gemma":[0.0005405368,0.0003237835,0.00004273029,0.000007297758,0.00001974401,0.00003790078,0.0001004397,0.003860206,0.3317857,0.0002899002,0.6626909,0.0003008826],"study_design_candidate":"not_applicable","study_design_consensus":"not_applicable","genre_codex":"methods","genre_gemma":"methods","genre_scores_codex":[0.01808535,0.0002396465,0.9680201,0.0002514696,0.00007267569,0.0007640636,0.00001714363,0.00006014406,0.01248941],"genre_scores_gemma":[0.2171824,0.0001704897,0.7697216,0.003882776,0.0002531729,0.0003385602,0.0007411927,0.00006781312,0.007642065],"genre_candidate":"methods","genre_consensus":"methods","teacher_disagreement_score":0.199097,"threshold_uncertainty_score":0.5346847,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.05379762823424428,"score_gpt":0.2991767766964953,"score_spread":0.245379148462251,"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."}}