Difference between revisions of "Run dbcan"
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(Created page with "Category:SoftwareCategory:Biology {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|run_dbcan}} |{{#vardefine:url|https://github.com/linnabrown/run_dbcan}} <!--CONFIG...") |
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|{{#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--> | ||
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| − | |{{#vardefine:citation|}} <!--CITATION--> | + | |{{#vardefine:citation|1}} <!--CITATION--> |
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(1) CAZyme substrate prediction based on '''dbCAN-sub'''; and | (1) CAZyme substrate prediction based on '''dbCAN-sub'''; and | ||
| − | (2) CGC substrate prediction based on '''dbCAN-PUL''' searching and '''dbCAN-sub''' majority voting. | + | (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. |
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| − | For CGC substrate prediction, please see the '''dbCAN-seq''' paper by [https://doi.org/10.1093/nar/gkad328 Zheng et al. 2023] for details. | ||
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==System Variables== | ==System Variables== | ||
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory | ||
| + | * HPC_{{uc:{{#var:app}}}}_BIN - executable directory | ||
| + | * HPC_DBCAN_REF - reference directory | ||
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<!--Configuration--> | <!--Configuration--> | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
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{{#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 | ||
|}} | |}} | ||
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If you publish research that uses {{#var:app}} you have to cite it as follows: | If you publish research that uses {{#var:app}} 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 | + | [https://doi.org/10.1093/nar/gky418 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] |
|}} | |}} | ||
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: