{"id":"W1493047563","doi":"10.1139/o06-143","title":"QUASI analysis of the HIV-1 envelope sequences in the Los Alamos National Laboratory HIV sequence database: pattern and distribution of positive selection sites and their frequencies over yearsThis paper is one of a selection of papers in this Special Issue, entitled International Symposium on Recent Advances in Molecular, Clinical, and Social Medicine, and has undergone the Journal's usual peer-review process.","year":2007,"lang":"en","type":"article","venue":"Biochemistry and Cell Biology","topic":"HIV Research and Treatment","field":"Immunology and Microbiology","cited_by":17,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Manitoba","funders":"","keywords":"Biology; Human immunodeficiency virus (HIV); Sequence database; Population; Virology; Selection (genetic algorithm); Sequence (biology); Clade; Conserved sequence; National laboratory; Genetics; Database; Gene; Peptide sequence; Phylogenetics; Physics; Medicine","routes":{"ca_aff":true,"ca_fund":false,"ca_venue":true,"about_ca":false,"invisible_to_affiliation_only":false},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0009265499,0.0001511849,0.0002458734,0.003314785,0.0004128654,0.0005460235,0.0001709652,0.0001992002,0.001153783],"category_scores_gemma":[0.003025834,0.0001060876,0.0002566661,0.003952723,0.0001791262,0.0004420332,0.0002929078,0.0002683971,0.0003513267],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0002159379,"about_ca_system_score_gemma":0.0004419092,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001891295,"about_ca_topic_score_gemma":0.004501642,"domain_scores_codex":[0.9994437,0.0001453048,0.00008514204,0.0001628395,0.0001265309,0.00003644952],"domain_scores_gemma":[0.9972452,0.00110716,0.0007562386,0.0002354439,0.0004724606,0.0001836278],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.001526155,0.0001468562,0.7512575,0.0007496949,0.0004011536,0.0005676431,0.001047688,0.001509024,0.116105,0.0007608392,0.004576655,0.1213518],"study_design_scores_gemma":[0.00002895782,0.0003209981,0.9670254,0.00004652341,0.0001238893,0.002274781,0.0005330621,0.007855879,0.01070437,0.0003757314,0.01067751,0.00003284689],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.986762,0.001122042,0.002901401,0.00005721826,0.00001558969,0.00003165904,0.008084662,0.0001537427,0.0008715978],"genre_scores_gemma":[0.9678264,0.0006081548,0.009226611,0.00004612855,0.00001730157,0.00006058512,0.02162832,0.00004855979,0.0005379835],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.003314785,"threshold_uncertainty_score":0.004900157,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02184124237447761,"score_gpt":0.3192354207616038,"score_spread":0.2973941783871262,"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."}}