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run_dbcan

Description

run_dbcan website

run_dbcan is tool for CAZyme and CGC substrate prediction based on dbCAN-sub and dbCAN-PUL searching and dbCAN-sub majority voting, respectively.

Environment Modules

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

Environment Variables

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

Additional Usage 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 --db_dir $HPC_DBCAN_REF/db

Citation

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. http://doi.org/10.1093/nar/gky418

Categories

biology