{"id":"W2118670112","doi":"10.1093/molbev/msi238","title":"Statistical Alignment of Retropseudogenes and Their Functional Paralogs","year":2005,"lang":"en","type":"article","venue":"Molecular Biology and Evolution","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":8,"is_retracted":false,"has_abstract":true,"ca_institutions":"Université de Montréal","funders":"","keywords":"Biology; Pseudogene; Genetics; Gene; Homology (biology); Stop codon; Computational biology; Most recent common ancestor; Sequence (biology); Molecular evolution; Coding region; Phylogenetic tree; Evolutionary biology; Genome","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":[0.00009182347,0.00009682368,0.000109093,0.00002204375,0.00005815802,0.000002743565,0.00003124535,0.0001043603,0.00000472629],"category_scores_gemma":[0.00002136374,0.00007982923,0.00002557957,0.00002061785,0.0002093906,5.010424e-7,0.00007460314,0.00002972295,8.894231e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000006467122,"about_ca_system_score_gemma":0.00001610402,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00001130429,"about_ca_topic_score_gemma":0.00001006048,"domain_scores_codex":[0.9994629,0.00004850523,0.0001243876,0.0002148252,0.00002549711,0.0001238691],"domain_scores_gemma":[0.9997826,0.000009801583,0.00003870706,0.00009825722,0.00003333432,0.00003726116],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","study_design_scores_codex":[0.00005216337,0.00002123218,0.03546225,0.00000587245,0.00006535682,2.199107e-7,0.00001796802,0.00003783112,0.9502262,0.01118692,0.0001162362,0.002807723],"study_design_scores_gemma":[0.001062698,0.001004819,0.6379982,0.000008001491,0.00005535171,0.00007253083,0.0001277859,0.0003754288,0.3323126,0.01351077,0.01312418,0.0003476399],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9459961,0.007742164,0.04579949,0.000181348,0.00004809605,0.00006537142,0.00004396766,0.000001688618,0.0001218016],"genre_scores_gemma":[0.9974008,0.000461943,0.001858816,0.0001086419,0.00007166473,0.000008800161,0.00005900058,0.000005510577,0.00002479917],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.6179137,"threshold_uncertainty_score":0.3255342,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.007119364549538367,"score_gpt":0.2286564585350696,"score_spread":0.2215370939855313,"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."}}