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:

Select a sequence in the Overview or Sequences view, then do any of the following:

  • 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.

Task How To
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:

  • Drag the left or right sequence wheels (gray/white areas under the text boxes) to scroll to a position of interest. A parenthesis denotes each currently selected endpoint. Click on a base or amino acid to snap to that position or drag the sequence wheels left or right to move the parenthesis to a different position. If the sequence is long, you can scroll along it more quickly by using the sliders under each wheel or by dragging the features/ruler wheels below the sliders.

  • Type a position into the text boxes above the left and right ends of the sequence. You can reference a numerical position, the left end (“lend”) or right end (“rend”) of the sequence, or a simple numeric expression. For example, lend+12 references the base that is 12 places to the right of the left end (i.e., position 1), while 815-27 references the base that is 27 places to the left of position 815.

  • Select the range corresponding to a feature by scrolling until the feature is visible under both sequence wheels. Then double-click on the same feature name under both the left and right wheels.
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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