Hualin Liu1, Jinshui Zheng1,2, Dexin Bo1,2, Yun Yu1, Weixing Ye1, Donghai Peng1, Ming Sun1. 1. State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China. 2. Hubei Key Laboratory of Agricultural Bioinformatics, Huazhong Agricultural University, Wuhan, 430070, China.
Abstract
SUMMARY: Bacillus thuringiensis (Bt) has been used as the most successful microbial pesticide for decades. Its toxin genes are used for the development of GM 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. AVAILABILITY AND IMPLEMENTATION: 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. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
SUMMARY:Bacillus thuringiensis (Bt) has been used as the most successful microbial pesticide for decades. Its toxin genes are used for the development of GM 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. AVAILABILITY AND IMPLEMENTATION: 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. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.