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The GenDB CORE documentation is intended to provide some general background knowledge about the GenDB annotation system. You should read the following chapters if you are planning to setup the system in order to annotate genomes.  
The GenDB CORE documentation is intended to provide some general background knowledge about the GenDB annotation system. You should read the following chapters if you are planning to setup the system in order to annotate genomes.  


* [[The first section]] describes the most important scripts for running a standard genome annotation pipeline.
* [[GenDBWiki/CoreDocumentation/CoreScripts|CoreScripts]]: This section describes the most important scripts for running a standard genome annotation pipeline.
* [[In this part]] you can find a number of details about the GenDB region prediction components.
* [[GenDBWiki/CoreDocumentation/RegionPrediction|RegionPrediction]]: In this part you can find a number of details about the GenDB region prediction components.
* Tools used for function prediction within the GenDB system are described here.
* [[GenDBWiki/CoreDocumentation/FunctionPrediction|FunctionPrediction]]: Tools used for function prediction within the GenDB system are described here.
* Additional scripts for special purpose tasks are explained in this last section of the GenDB CORE documentation.
* [[GenDBWiki/CoreDocumentation/AdditionalScripts|AdditionalScripts]]: Additional scripts for special purpose tasks are explained in this last section of the GenDB CORE documentation.


This section describes the basic steps for automatically annotating a genome using the scripts provided with the GenDB CORE package. Each script has a detailed usage message that is displayed when a script is executed without any arguments. Please take a look at the documentation of each script for alternative options or advanced features.
For writing your own programs using the GenDB API please take a look at the GenDB developer section and the API documentation.
 
* ''import_EMBL_GBK.pl'' -
* ''tool_creator.pl''
* ''submit_job.pl''
* ''export_EMBL_GBK.pl''
* ''delete_contig.pl''
* ''delete_contig_with_feedback.pl''
 
In addition to the scripts required for annotating a genome the GenDB CORE package includes a number of scripts for maintaining GenDB databases and projects listed below:
 
* ''add_annotator.pl'' - This script can be used for adding a human annotator to a GenDB project database. Usually this is already done automatically by the GPMS.
* ''cleanup_database.pl'' - This script checks a number of GenDB objects for consistency. Objects with illegal references e.g. to already deleted objects are removed and deleted automatically.
* ''optimize_tables.pl'' - Use this script after larger database operations like computing several tools in order to optimize all tables automatically.
* ''set_user_config.pl'' - A default user configuration can be transferred to a GenDB user account with this script.

Latest revision as of 10:20, 28 October 2011

GenDB CORE Documentation

The GenDB CORE documentation is intended to provide some general background knowledge about the GenDB annotation system. You should read the following chapters if you are planning to setup the system in order to annotate genomes.

  • CoreScripts: This section describes the most important scripts for running a standard genome annotation pipeline.
  • RegionPrediction: In this part you can find a number of details about the GenDB region prediction components.
  • FunctionPrediction: Tools used for function prediction within the GenDB system are described here.
  • AdditionalScripts: Additional scripts for special purpose tasks are explained in this last section of the GenDB CORE documentation.

For writing your own programs using the GenDB API please take a look at the GenDB developer section and the API documentation.

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