Difference between revisions of "Run dbcan"
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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: | 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 | + | run_dbcan EscheriaColiK12MG1655.fna prok --out_dir output_EscheriaColiK12MG1655 --use_signalP=TRUE --db_dir $HPC_DBCAN_REF/db |
|}} | |}} | ||
Latest revision as of 20:06, 23 September 2024
Description
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 --db_dir $HPC_DBCAN_REF/db
Citation
If you publish research that uses run_dbcan you have to cite it as follows: