{"id":"W1976876832","doi":"10.1186/1471-2164-14-502","title":"Transposon fingerprinting using low coverage whole genome shotgun sequencing in Cacao (Theobroma cacao L.) and related species","year":2013,"lang":"en","type":"article","venue":"BMC Genomics","topic":"Chromosomal and Genetic Variations","field":"Agricultural and Biological Sciences","cited_by":19,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of British Columbia","funders":"Natural Sciences and Engineering Research Council of Canada; World Bank Group","keywords":"Theobroma; Biology; Shotgun sequencing; Genome; Transposable element; Sequence assembly; Genome size; Germplasm; Reference genome; Phylogenetic tree; Genomics; DNA sequencing; Genome evolution; Genetics; Evolutionary biology; Retrotransposon; Computational biology; Gene; Botany","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":[0.0003342505,0.0002706244,0.0002734489,0.001525555,0.0004374637,0.0003999517,0.0003384594,0.0004543796,0.0006129555],"category_scores_gemma":[0.0006032058,0.0001096218,0.0003541857,0.0009701849,0.0002075749,0.0001741137,0.0002175326,0.0002030406,0.0002254359],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0005912207,"about_ca_system_score_gemma":0.0002491306,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.01000641,"about_ca_topic_score_gemma":0.01259075,"domain_scores_codex":[0.9998075,0.00001431098,0.00001469505,0.0001001596,0.00004120856,0.00002208204],"domain_scores_gemma":[0.9997042,0.00006446404,0.00007039527,0.00002409217,0.00009504118,0.00004182133],"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":[0.000184031,0.00004034775,0.02324424,0.0001767372,0.00004703451,0.0001802029,0.0006005445,0.0002281437,0.9630677,0.00009253341,0.00006792207,0.01207056],"study_design_scores_gemma":[0.00001955436,0.0004786833,0.8741598,0.0000524302,0.000224526,0.001433138,0.0008034031,0.003686404,0.1136442,0.000212005,0.005242737,0.00004307989],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9952788,0.0004683769,0.00223728,0.00002556089,0.00000921346,0.00003857409,0.001190899,0.00007202871,0.0006792874],"genre_scores_gemma":[0.9790325,0.0003655116,0.01470771,0.0000934217,0.00001177683,0.00007036067,0.004219658,0.00005187061,0.001447119],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.01000641,"threshold_uncertainty_score":0.01989633,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02453586678725984,"score_gpt":0.1958144466327474,"score_spread":0.1712785798454875,"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."}}