Database files

PlasmidTools sequence databases are customizable databases containing unambiguous sequences, such as the T7 promoter sequence and the b-lactamase (ampR) gene. The program comes with three pre-made databases: antibiotic resistance genes, Gateway recombination sites, and an (almost) empty database named CustomSequenceDatabase. The latter is set as the default target database for receiving new entries, but this can be changed as needed (Sequence Db menu - Target database).

Database files are stored in the "PlasmidToolsData" directory, which is created in "My documents" when PlasmidTools is installed. New databases created in the "Database Manager" must be saved in this directory in order to be accessible to the program.

It is possible to set a new storage location for the "PlasmidToolsData" directory by running the "Sequence database setup" procedure (SequenceDb menu). This will create a new "PlasmidToolsData" directory in a selected location together with a copy of the previous "CustomSequenceDatabase" file, if present. Other database files must be copied manually. If the selected storage location contains a database folder and file it will be linked to and not modified.

Managing contents

The "Sequence Db manager" (SequenceDb menu) is used to open database files and edit their contents. Entries may be created, edited, deleted, and copied between database files.

New entries may also be added from the "Annotation manager" window displaying annotated features in an open project file. By selecting one or more (Ctrl+click) entries in the annotation manager and then click the "Add to sequence database" button , the selected features are copied to the target database. Naturally, only annotations of the region type, defining a recognition sequence, can be added this way. The "Annotation manager" also has a button to choose the target database for receiving new entries.

Scan project files

The "Scan project.." function scans an open project for sequences matching those stored in sequence databases. For databases to be included in scanning they must be selected in the "Sequence Db scan filter" (Sequence Db menu). Db scanning may also detect degenerate sequences by setting the identity threshold in the toolbar to a value below 100 %. Results are displayed in the results table and are annotated in the usual way; select one or more (Ctrl+click) features (rows) and click the Annotate button .