Project cleanup

The clean-up tool removes non-sequence characters often found in pasted sequences, like punctuation, numbers, blanks and line breaks. Run it directly after text has been pasted in the sequence pane. Annotations contained between brackets <…> are ignored in the cleaning process. Make sure that any annotations are correctly enclosed in brackets <…> before doing clean-up. If not, the program will not be able to distinguish between annotations and the sequence itself and produce unexpected results. When cleaning up an existing project file it may be a good idea to run the "Checkup" function first, and examine the report. For example, a row of invalid bases like "o I / >" could indicate a missing "<" in front of "EcoRI/>". The cleanup removes characters not conforming to the IUPAC nomenclature for DNA/RNA/protein residues and ambiguity symbols.

Project checkup

The Checkup function will analyse the project for errors in base composition and annotations and display a report.

Composition – Sequence must conform to the IUPAC nomenclature for DNA/RNA/protein residues and ambiguity symbols. Other characters will be listed in the error report. Annotations are ignored in this test.

Annotations – The test will detect many inconsistencies in annotation syntax. In some situations, it may also identify the problem and suggest a solution.

Managing annotations

Results from analysis functions are displayed in the multi-purpose pane as tabular data. By selecting one or more (Ctrl+click) rows and then click on the annotate button (in the results pane or a right-click menu), the selected features are annotated in the project file/graphical map in correct position and configuration.

Annotations may also be added directly in the sequence pane. To annotate a sequence range, select (drag over) the sequence and click on "Annotate selection" in the right-click menu. In the pop-up, fill in name and direction. To annotate a specific position, place the cursor in the position and click on "Insert <>" in the right-click menu, and type in a name followed by "/" inside the brackets.

The "Manage annotations" button is used to display a list of all annotations contained in the project file. Entries can be edited, deleted, copied to a sequence database, and new ones can be created by filling in required information.

There is also the possibility to edit annotations by manual editing in the sequence pane. Make sure to follow the annotation rules if doing manual edits (see below). However, this is not a recommended method for handling annotations (exept when fixing bugs). PlasmidTools has all the functionality needed to handle annotations programatically, which is safer.

The names of annotated restriction-enzyme cut sites should not be modified, but appear exactly as displayed in the enzyme list. The names are used by program functions to look up enzyme properties, for example to position cut sites when switching strands (reverse complement), in which the type and length of the overhang must be known.

Annotation rules/syntax:

Specific point in sequence (cut site etc.)	<name/>
Region without direction	<name>...</name>
Region in forward direction	<+name>...</name>
Region in reverse direction	<-name>...</name>
ORF in forward direction	<++name>...</name>
ORF in reverse direction	<--name>...</name>