Run dbcan

Jump to navigation Jump to search


run_dbcan website  

run_dbcan is the standalone version of dbCAN annotation tool for automated CAZyme annotation. The application is useful for the following:

(1) CAZyme substrate prediction based on dbCAN-sub; and

(2) CGC substrate prediction based on dbCAN-PUL searching and dbCAN-sub majority voting. For CGC substrate prediction, please see the dbCAN-seq paper by Zheng et al. 2023 for details.

Environment Modules

Run module spider run_dbcan to find out what environment modules are available for this application.

System Variables

  • HPC_RUN_DBCAN_DIR - installation directory
  • HPC_RUN_DBCAN_BIN - executable directory
  • HPC_DBCAN_REF - reference directory

Additional Information

Note: This installation also includes SignalP (version 4.1) peptide prediction. Use the flag --use_signalP=True as in the following example to run SignalP with run_dbcan:

run_dbcan EscheriaColiK12MG1655.fna prok --out_dir output_EscheriaColiK12MG1655 --use_signalP=TRUE


If you publish research that uses run_dbcan you have to cite it as follows:

Han Zhang, Tanner Yohe, Le Huang, Sarah Entwistle, Peizhi Wu, Zhenglu Yang, Peter K Busk, Ying Xu, Yanbin Yin; dbCAN2: a meta server for automated carbohydrate-active enzyme annotation, Nucleic Acids Research, Volume 46, Issue W1, 2 July 2018, Pages W95–W101. doi: 10.1093/nar/gky418