Manual > Files & formats

Files & formats

• PlasmidTools file types
• Windows integration
• Create new projects
• Import of sequence files
• Import of non-standard file types
• Export to other formats

PlasmidTools file types

PlasmidTools has three associated file types: project (*.ptools), alignment (*.ptalign) and sequence database (*.seqdb). A project file holds one sequence with annotations and settings. An alignment file holds one reference sequence and as many sequence reads as required. Project and alignment files should be organized in folders just like other documents. Database files can store as many sequence entries as desired, and must be stored in the "PlasmidToolsData" directory which is created during program installation.

Windows integration

PlasmidTools file types are registered types in Windows and have the usual double-click and right-click functionality and associated icons. A double-click on a .ptools file launches PlasmidTools and the clicked project. A double-click on a .ptalign or .seqdb file launches PlasmidTools and a message window explaining that these files must be opened in the respective module inside PlasmidTools.

The file-type associations are handled by the " ClickOnce Application Deployment Support Library", which must be set as the default program for opening PlasmidTools files by double-click in Windows Explorer. This is configured when PlasmidTools is installed.

Create new projects

New projects are created by clicking the "New project" button . A sequence may then be typed or pasted in the sequence pane. After adding text/sequence it is strongly recommended to run the Cleanup tool to remove non-sequence characters and punctuation like spaces and linebreaks. Subsequently, fill in a name, set the sequence type (DNA, RNA or protein) and configuration (linear or circular), and save the new project.

For existing sequences already stored in sequence files like FastA and Genbank files, use the import function to create a new project.

Import of sequence files

File import is started by clicking the "Import" button . Imported files are converted to PlasmidTools projects and opened in new project tabs in the sequence pane. The sequence format is detected automatically based on the file's contents, irrespective of file type/extension. This facilitates opening of non-standard file types like *.seq, which may have different internal formats. The filtering options in the Open dialog merely affects which files are shown in the list based on file extension. The analysis/detection of sequence format is independent of file type/extension.

Supported formats for import are: plain sequence, FastA, GenBank, EMBL, IG and GCG (only GCG files created in GCG are suitable for import. Files imported or converted in GCG often have a mixed format). Import of annotations from GenBank and EMBL files is limited to the CDS (coding sequence) sections. With other formats, only the sequence is imported.

To import sequence files not covered by auto-detection, see the section "Import of non-standard file types" below.

Import of non-standard file types

For import of unsupported types, or files containing multiple sequences, or damaged syntax, follow the procedure below (note that this applies to plain-text files, those readable in a text editor, not binary or encrypted files):

1. Click the "New" button to add a new project.
2. Click the Text Editor button and open the file containing the sequence.
3. Select the lines containing the DNA/RNA/aa sequence and click the Copy button (or use Ctrl+C). Do not include alphabetical letters that are not part of the sequence. (If you do, delete it in step 4).
4. Click in the sequence pane to make it active and select Paste (or use Ctrl+V).
5. Click the "Clean-up" (rubber) button to remove non-sequence characters and punctuation.
6. Enter a descriptive name in the name box.
7. Select correct sequence type and configuration (linear/circular) in the toolbar pull-down lists.
8. Click the "Save as.." button to save the new project.
9. Optionally, use the "Check" button to analyse project for errors.

Export to other formats

The "File - Export" function exports the active project to the selected format. The alternatives are Plain sequence, FastA, GenBank and EMBL. The exported sequence opens in a Text Editor window, from which it can be modified and saved to file, or copied to a document.