Individual sequences in the project can be trimmed before or after alignment based on features or by direct selection. This is different from trimming the entire alignment, which affects all sequences in the project.
To trim an individual sequence before or after performing an alignment:
- Press the Trim Sequence tool () from the toolbar.
- Choose Sequences > Trim Sequence.
- Right-click on the sequence and choose Trim Sequence.
The Trim Sequences dialog opens.
The left and right halves of the dialog are used to specify the desired left and right sequence ends. On each side, the uppermost section is a textbox showing the currently-selected endpoint. Initially, these boxes are populated with the first and last nucleotides or amino acids in the sequence.
The following table shows tasks that can be done from within this dialog, or that affect its appearance.
|To reveal/hide the sequence
|Click the green “up” arrow on the upper right of the popup.
|To reveal/hide the ruler and any features that are present
|Click the green “down” arrow on the upper right of the popup.
|To specify the desired range
| Use any of the following methods:
|To skip to the left or right ends of the sequence
| Click in a range text box, then use the gray left/right arrow icons that appear within the box. Alternatively, type in
lend (left end) or
rend (right end).
|To view feature information
|Hover above a feature (if any are present) to see information about it, such as its left and right coordinates.
|To reverse complement the current sub-range
|Click the green arrow between the two range textboxes.
IUPAC ambiguity codes are recognized both in the sequence and in the range boxes. For example, typing AAS (where S = C or G) into a range box would cause SeqNinja to look for the first instance of AAC or AAG in the sequence. Conversely, typing AAC into a range box would cause SeqNinja to look for the first instance of AAC, as well as any combination of bases and ambiguity codes that would allow for AAC (e.g., AAS, WWM, etc.).
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