{"id":"W1990064224","doi":"10.1186/1756-0500-2-14","title":"Sequence Searcher: A Java tool to perform regular expression and fuzzy searches of multiple DNA and protein sequences","year":2009,"lang":"en","type":"article","venue":"BMC Research Notes","topic":"RNA and protein synthesis mechanisms","field":"Biochemistry, Genetics and Molecular Biology","cited_by":16,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Victoria","funders":"National Institute of Allergy and Infectious Diseases","keywords":"Computer science; Sequence (biology); Set (abstract data type); Java; Data mining; Matching (statistics); Fuzzy logic; Feature (linguistics); Limiting; Approximate string matching; Regular expression; Computational biology; Nearest neighbor search; Bioinformatics; Information retrieval; Pattern matching; Artificial intelligence; Biology; Genetics; Programming language; Mathematics","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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.001822114,0.001392131,0.001239811,0.001988722,0.0006293724,0.001127511,0.002340411,0.001011355,0.03451957],"category_scores_gemma":[0.002882166,0.0009399246,0.001223194,0.0009390877,0.0005544733,0.001633052,0.001346757,0.001102989,0.01774394],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0005409032,"about_ca_system_score_gemma":0.001119139,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001273755,"about_ca_topic_score_gemma":0.00220152,"domain_scores_codex":[0.9991862,0.0001069601,0.000147362,0.0001891354,0.0003023465,0.00006798583],"domain_scores_gemma":[0.9985354,0.0008133094,0.0001798385,0.0001521816,0.000215499,0.0001038143],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"design_other","study_design_gemma":"not_applicable","study_design_scores_codex":[0.002019199,0.0004207984,0.004945483,0.00385509,0.0003940415,0.001508296,0.0005530072,0.006249551,0.2183467,0.01650202,0.2196832,0.5255225],"study_design_scores_gemma":[0.001368219,0.0006028291,0.0101777,0.0006659874,0.0002271597,0.004553985,0.0002699017,0.2909839,0.2581006,0.04542202,0.387012,0.0006157426],"study_design_candidate":"not_applicable","study_design_consensus":null,"genre_codex":"methods","genre_gemma":"software","genre_scores_codex":[0.00502135,0.0002482993,0.7239353,0.0001478598,0.00009196885,0.0002873939,0.00770344,0.2593855,0.003179],"genre_scores_gemma":[0.03488616,0.0003301205,0.9128323,0.0003632653,0.00005563261,0.0008531968,0.01439365,0.02646242,0.009823257],"genre_candidate":"software","genre_consensus":null,"teacher_disagreement_score":0.03451957,"threshold_uncertainty_score":0.1154795,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.1220691926556259,"score_gpt":0.3636630721064739,"score_spread":0.241593879450848,"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."}}