{"id":"W2100258314","doi":"10.1186/1471-2105-5-96","title":"Base-By-Base: Single nucleotide-level analysis of whole viral genome alignments","year":2004,"lang":"en","type":"article","venue":"BMC Bioinformatics","topic":"Poxvirus research and outbreaks","field":"Immunology and Microbiology","cited_by":80,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Victoria","funders":"National Institute of Allergy and Infectious Diseases; Natural Sciences and Engineering Research Council of Canada; Defense Advanced Research Projects Agency","keywords":"Genome; Annotation; Biology; Computational biology; Java; Gene; Genome browser; Genetics; DNA microarray; Computer science; Software; Genomics; Programming language","routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"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":[0.004358171,0.003007497,0.002425728,0.006604678,0.001296256,0.002875396,0.002927298,0.001518962,0.02793374],"category_scores_gemma":[0.01306986,0.001263698,0.001936959,0.006637902,0.0005342117,0.002730261,0.001688783,0.002456138,0.01693022],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0006121618,"about_ca_system_score_gemma":0.001454577,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001441946,"about_ca_topic_score_gemma":0.00168205,"domain_scores_codex":[0.9977913,0.0004402944,0.0002331031,0.0006467814,0.0007539545,0.0001345545],"domain_scores_gemma":[0.9950648,0.002172045,0.0008155247,0.0007595076,0.0008960455,0.0002920555],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"not_applicable","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.00490731,0.001292072,0.02486597,0.005298409,0.002552117,0.00170515,0.001820547,0.01051384,0.1424001,0.008168875,0.4094854,0.3869902],"study_design_scores_gemma":[0.001187421,0.001456033,0.05778284,0.000830117,0.001278442,0.004894084,0.0006031414,0.3894106,0.1623375,0.03133624,0.347867,0.001016647],"study_design_candidate":"simulation_or_modeling","study_design_consensus":null,"genre_codex":"methods","genre_gemma":"methods","genre_scores_codex":[0.03374828,0.0009691216,0.499157,0.0003728881,0.000693616,0.0005789798,0.0710332,0.3881913,0.005255786],"genre_scores_gemma":[0.07731955,0.0005158957,0.7702422,0.0002209245,0.0001771424,0.001152436,0.0968245,0.05155588,0.00199148],"genre_candidate":"methods","genre_consensus":"methods","teacher_disagreement_score":0.02793374,"threshold_uncertainty_score":0.09344769,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.03318109257616441,"score_gpt":0.2569063753054517,"score_spread":0.2237252827292873,"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."}}