{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,18]],"date-time":"2026-08-18T15:53:24Z","timestamp":1787068404039,"version":"build-2736575974"},"reference-count":22,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2021,7,9]],"date-time":"2021-07-09T00:00:00Z","timestamp":1625788800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100012166","name":"National Key R&D Program of China","doi-asserted-by":"crossref","award":["2017YFD0201201"],"award-info":[{"award-number":["2017YFD0201201"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31670085"],"award-info":[{"award-number":["31670085"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31970003"],"award-info":[{"award-number":["31970003"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31770003"],"award-info":[{"award-number":["31770003"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,12,22]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>Bacillus thuringiensis (Bt) has been used as the most successful microbial pesticide for decades. Its toxin genes are used for the development of genetically modified crops against pests. We previously developed a web-based insecticidal gene mining tool BtToxin_scanner. It has been frequently used by many researchers worldwide. However, it can only handle the genome one by one online. To facilitate efficiently mining toxin genes from large-scale sequence data, we re-designed this tool with a new workflow and the novel bacterial pesticidal protein database. Here, we present BtToxin_Digger, a comprehensive and high-throughput Bt toxin mining tool. It can be used to predict Bt toxin genes from thousands of raw genome and metagenome data, and provides accurate results for downstream analysis and experiment testing. Moreover, it can also be used to mine other targeting genes from large-scale genome and metagenome data with the replacement of the database.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>The BtToxin_Digger codes and web services are freely available at https:\/\/github.com\/BMBGenomics\/BtToxin_Digger and https:\/\/bcam.hzau.edu.cn\/BtToxin_Digger, respectively.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btab506","type":"journal-article","created":{"date-parts":[[2021,7,7]],"date-time":"2021-07-07T07:20:44Z","timestamp":1625642444000},"page":"250-251","source":"Crossref","is-referenced-by-count":38,"title":["BtToxin_Digger: a comprehensive and high-throughput pipeline for mining toxin protein genes from\n                    <i>Bacillus thuringiensis<\/i>"],"prefix":"10.1093","volume":"38","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3630-5522","authenticated-orcid":false,"given":"Hualin","family":"Liu","sequence":"first","affiliation":[{"name":"State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University , Wuhan 430070, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0147-5900","authenticated-orcid":false,"given":"Jinshui","family":"Zheng","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University , Wuhan 430070, China"},{"name":"Hubei Key Laboratory of Agricultural Bioinformatics, Huazhong Agricultural University , Wuhan 430070, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dexin","family":"Bo","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University , Wuhan 430070, China"},{"name":"Hubei Key Laboratory of Agricultural Bioinformatics, Huazhong Agricultural University , Wuhan 430070, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yun","family":"Yu","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University , Wuhan 430070, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Weixing","family":"Ye","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University , Wuhan 430070, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Donghai","family":"Peng","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University , Wuhan 430070, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5465-5983","authenticated-orcid":false,"given":"Ming","family":"Sun","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University , Wuhan 430070, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2021,7,9]]},"reference":[{"key":"2023020108385788200_btab506-B1","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1016\/B978-0-12-800197-4.00002-6","volume-title":"Advances in Insect Physiology, Insect Midgut and Insecticidal Proteins","author":"Adang","year":"2014"},{"key":"2023020108385788200_btab506-B2","doi-asserted-by":"crossref","first-page":"421","DOI":"10.1186\/1471-2105-10-421","article-title":"BLAST+: architecture and applications","volume":"10","author":"Camacho","year":"2009","journal-title":"BMC Bioinformatics"},{"key":"2023020108385788200_btab506-B3","doi-asserted-by":"crossref","first-page":"e00034","DOI":"10.1128\/mBio.00034-20","article-title":"Proposal of a taxonomic nomenclature for the Bacillus cereus group which reconciles genomic definitions of bacterial species with clinical and industrial phenotypes","volume":"11","author":"Carroll","year":"2020","journal-title":"mBio"},{"key":"2023020108385788200_btab506-B4","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1145\/1961189.1961199","article-title":"LIBSVM: a library for support vector machines","volume":"2","author":"Chang","year":"2011","journal-title":"ACM Trans. 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