Difference between revisions of "Run dbcan"
| (One intermediate revision by the same user not shown) | |||
| Line 5: | Line 5: | ||
<!--CONFIGURATION: OPTIONAL (|1}} means it's ON)--> | <!--CONFIGURATION: OPTIONAL (|1}} means it's ON)--> | ||
|{{#vardefine:conf|}} <!--CONFIGURATION--> | |{{#vardefine:conf|}} <!--CONFIGURATION--> | ||
| − | |{{#vardefine:exe|}} <!--ADDITIONAL INFO--> | + | |{{#vardefine:exe|1}} <!--ADDITIONAL INFO--> |
|{{#vardefine:job|}} <!--JOB SCRIPTS--> | |{{#vardefine:job|}} <!--JOB SCRIPTS--> | ||
|{{#vardefine:policy|}} <!--POLICY--> | |{{#vardefine:policy|}} <!--POLICY--> | ||
|{{#vardefine:testing|}} <!--PROFILING--> | |{{#vardefine:testing|}} <!--PROFILING--> | ||
|{{#vardefine:faq|}} <!--FAQ--> | |{{#vardefine:faq|}} <!--FAQ--> | ||
| − | |{{#vardefine:citation|}} <!--CITATION--> | + | |{{#vardefine:citation|1}} <!--CITATION--> |
|{{#vardefine:installation|}} <!--INSTALLATION--> | |{{#vardefine:installation|}} <!--INSTALLATION--> | ||
|} | |} | ||
| Line 23: | Line 23: | ||
(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 [https://doi.org/10.1093/nar/gkad328 Zheng et al. 2023] for details. | (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 [https://doi.org/10.1093/nar/gkad328 Zheng et al. 2023] for details. | ||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
<!--Modules--> | <!--Modules--> | ||
| Line 44: | Line 39: | ||
{{#if: {{#var: exe}}|==Additional Information== | {{#if: {{#var: exe}}|==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 | ||
|}} | |}} | ||
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: