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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(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.  
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(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.
 
 
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
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* HPC_{{uc:{{#var:app}}}}_BIN - executable directory
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* HPC_DBCAN_REF - reference directory
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{{#if: {{#var: exe}}|==Additional Information==
 
{{#if: {{#var: exe}}|==Additional Information==
  
WRITE_ADDITIONAL_INSTRUCTIONS_ON_RUNNING_THE_SOFTWARE_IF_NECESSARY
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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:
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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
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[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]
  
 
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Latest revision as of 20:06, 23 September 2024

Description

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 --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. doi: 10.1093/nar/gky418