GenDBWiki/CoreDocumentation

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.

• 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.