Add and modify a sequence

Many of the Templates panel and Toolkit panel items require you to choose a sequence file.

• Click the Choose Sequence(s) button to open a file chooser. Alternatively, you may type in the path and file name in the drop-down menu (or text box) to the right of that button. The sequence you enter will apply only within that step and not to subsequent steps.

• Use the plus and minus icons on the right to either add another sequence or to delete an existing sequence (see table, below).

*Notes:

About the yellow “warnings”: Until you choose a valid sequence, the drop-down menu (or text box) will be highlighted in yellow and may also display a triangular warning icon. Hovering over the sequence name displays a balloon tip: “WARNING: file not found.” This warning is normal and will disappear once you choose a valid sequence.

About the use of quotation marks in paths: If you are using the Text view, double-quotes should be used around most paths, whether in settings or sequence expressions. Double-quotes inside of paths, however, are not supported. When using the Visual view, use paths that do not contain double-quotes. Also, for File Pattern specification, single-quotes must be used to distinguish file patterns from individual file paths, which are double-quoted.

About “dependent” sequences: Within the same script, you may use the output sequence from an earlier step as the input sequence for a later step. However, the result might not be what you expected or desired. For example, if an extracted CDS initially had a /codon_start annotation (i.e., it did not start with an intact codon), that information would be lost in the extracted FASTA file. Then, when the file was subsequently translated, it would be in the wrong reading frame.

• The right-most drop-down menu, which is initially set to”(All sequences),” lets you further narrow down the sequence of interest by choosing one individual sequence from the selected file. Only the first 100 sequence names are displayed. To display additional sequences, click < more > at the bottom of the menu to bring up a chooser dialog. If no selection is made from the menu, the command will be executed on the entire file of sequences rather than on one individual sequence. Exception: when a sub-range or concatenation uses the file, and no selection is made, only the first sequence is used.

• The following tools are available to the right of any Choose Sequence(s) button row:

Tool	Function	Description
	Add	This button offers a sub-set of the “Add” items from the Sequences section.
	Remove	Depending on the operation, clicking this button offers one or more of the following choices: Remove, Delete, Undo.
	Modify	The pencil icon lets you modify an operation by nesting the current operation into a newly-selected one. The function modifies the sequence directly to the left of the icon. Depending on the operation, clicking this button lets you modify the selected item using shortcuts to Functions section items.

• For right-click menu options available in the Choose Sequence(s) button row, see the last table in Right-click functionality in the Visual view.