{"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":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0001396858,0.0001493881,0.0001848717,0.00002019546,0.0002155054,0.0001127452,0.0001399782,0.0001121514,0.0004388248],"category_scores_gemma":[0.00002340734,0.00007826007,0.00006107368,0.0002150205,0.00004458804,0.000132079,0.00006173922,0.0001311537,0.00004452328],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001657199,"about_ca_system_score_gemma":0.00002976987,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001472362,"about_ca_topic_score_gemma":0.002060309,"domain_scores_codex":[0.998946,0.00005264246,0.000299953,0.0003020879,0.00009167758,0.0003076041],"domain_scores_gemma":[0.9996433,0.0001012739,0.0000838149,0.00006130191,0.00002823344,0.00008213575],"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":[0.000003622745,0.00001527734,0.01791389,0.00001098425,0.00000565364,0.000003245278,0.0008527741,0.003112226,0.9765733,0.00007490267,0.000001109577,0.00143305],"study_design_scores_gemma":[0.0003381153,0.00006139409,0.9732292,0.00005123364,0.00001967676,0.00003929786,0.001109712,0.01434148,0.006278185,0.002982859,0.001137141,0.0004117631],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.998533,0.0001630988,0.00002572556,0.0001728105,0.00006919442,0.0002915562,0.00003737877,0.00003048554,0.0006767166],"genre_scores_gemma":[0.9984791,0.0000475607,0.0009730618,0.00005627002,0.0001069908,0.000008103586,0.00003866714,0.000002413529,0.000287857],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.9702951,"threshold_uncertainty_score":0.4804824,"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."}}