{"id":"W4416147727","doi":"10.1007/s11756-025-02057-5","title":"OligoDesign: enchancing primer specificity through multi-sequence aligment and validation","year":2025,"lang":"en","type":"article","venue":"Biologia","topic":"Biosensors and Analytical Detection","field":"Engineering","cited_by":0,"is_retracted":false,"has_abstract":false,"ca_institutions":"Dalhousie University","funders":"","keywords":"In silico; Amplicon; Primer (cosmetics); Oligonucleotide; In silico PCR; Selection (genetic algorithm); DNA sequencing; Sequence (biology)","routes":{"ca_aff":true,"ca_fund":false,"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":[0.00007375329,0.00007745437,0.00008557174,0.00002500563,0.00004287117,0.00001856853,0.00003590282,0.00008144168,0.00001199243],"category_scores_gemma":[0.00002232956,0.00006361857,0.00001995407,0.0001007148,0.00003180255,0.00004489083,0.00001675595,0.00006551446,0.00001199706],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000042797,"about_ca_system_score_gemma":0.000003780345,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00003127961,"about_ca_topic_score_gemma":0.000003176026,"domain_scores_codex":[0.9995991,0.00001545985,0.0001093439,0.000132303,0.00003061424,0.0001131503],"domain_scores_gemma":[0.9998533,0.00002441609,0.00001132162,0.00007991483,0.00001471269,0.00001633696],"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":[0.000005618985,0.00001712613,0.00264991,0.00005470602,0.00003265483,0.000001689759,0.00005443854,0.0006562062,0.9813677,0.003600487,0.0003379199,0.01122151],"study_design_scores_gemma":[0.0001896826,0.0000334535,0.01729774,0.00005187449,0.00001749278,0.000001741221,0.00004851267,0.03671313,0.9412891,0.0009918503,0.003188292,0.0001771393],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.7788273,0.0005671003,0.217752,0.0001019504,0.0004000317,0.0001541454,0.00000596799,0.0002553086,0.001936162],"genre_scores_gemma":[0.9950078,0.0002630524,0.004496011,0.00005116224,0.00003459409,0.000004959702,0.000003544128,0.00000374845,0.0001351583],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.2161804,"threshold_uncertainty_score":0.259429,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.04633975919759269,"score_gpt":0.2782386911662478,"score_spread":0.2318989319686551,"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."}}