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 |
---|---|
Reveal/hide the sequence | Click the green “up” arrow on the upper right of the popup. |
Reveal/hide the ruler and any features that are present | Click the green “down” arrow on the upper right of the popup. |
Specify the desired range | Use any of the following methods:
|
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). |
View feature information | Hover above a feature (if any are present) to see information about it, such as its left and right coordinates. |
Reverse complement the current sub-range | Click the green arrow between the two range textboxes. |
Example expressions:
Expression | Meaning |
---|---|
lend>>“ATG” | Start at the left end and search on the forward strand for ATG. When using a lend expression, the resulting position is the left side of the match. |
rend<<“CTA” | Start at the right end and search the reverse strand for CTA (which matches TAG on the forward strand). When using a rend expression, the resulting position is the right side of the match. |
ATG | References the first occurrence of the string ATG. |
ATG+3 | References a six-base region starting at that “A” in the ATG and moving to the right. |
ATG in the left end box and TAG in the right end box | References the region starting from the “A” in ATG, and ending with the “G” in TAG. |
lend_>>“ATG”>>“TAG” | References the first TAG after the first ATG. |
1000>>“ATG” | References the first ATG at or after position 1000. |
lend>>“ATG” + 3 | References three residues past the left side of the first ATG. |
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