In the Alignment view, you may edit constituent or consensus sequences in an .sqd project contig by removing or adding nucleotides or gaps.

Task How To
Remove or add gaps Insert the cursor into an individual sequence and type one or more dashes (-) or delete the same. The consensus sequence will be recalculated to reflect your changes.
Remove or add nucleotides using the keyboard To remove nucleotides, insert your cursor in the desired location and use the Backspace or Delete keys.

To add nucleotides, insert your cursor and begin typing. When you add new nucleotides, they will appear in lower case to signify a manual addition.

If you edit one or more constituent sequences, the consensus sequence will be recalculated to reflect your changes.

If you add nucleotides to or delete them from the consensus and then restore a trimmed constituent sequence in the same region, the restored sequence will not reflect the insertion/deletion. If you want to ensure that all sequences reflect the changes to the consensus sequence, you should restore trimmed data (see row below) before editing the consensus sequence.

Note: If you attempt to add or remove nucleotides using this method, you may receive the following warning:

If you still wish to proceed, click OK.
Change the trim points on sequence ends Before trimming or restoring data, you will likely want to display the trace data first. This can be done by clicking the plus sign () to the left of each sequence name. Sequences with trimmed ends will have a small triangle at one or both ends of the sequence. To trim or restore sequence, use any of the following methods:

  • Drag the triangle manually to either side to reveal previously-trimmed sequence or to trim the sequence even more.

  • Automatically trim more sequence by right-clicking at the point where you wish to trim the sequence and choose Trim the Left/Right End of This Read to Here or Trim the Left/Right End of All Reads to Here. The availability of Left, Right or both options in the command names depends on where you right-click on the sequence.

  • Automatically restore some or all trimmed sequence by right-clicking and choosing Untrim the Left/Right End of This Read or Untrim the Left/Right End of All Reads. The availability of Left, Right or both options depends on where you right-click on the sequence.
Cut or copy a selected portion of the sequence Select some or all of the sequence, then right-click and choose Cut or Copy.
Slide a Sanger sequence relative to other sequences Use the Banana tool (). in the Alignment view header. When this tool is activated, the cursor is shaped like a banana. Use your mouse and the banana-shaped cursor to drag any sequence in the Alignment view to the left or right, as desired. When you are done, click the Banana tool again to return the cursor to its normal state. Note that this tool is only active when the alignment contains Sanger trace files.
Remove a selected sequence from the contig Select a sequence name at the left of the Alignment view, then choose Sequence > Remove Sequence.

Note that changes made to a constituent sequence only directly affect that sequence, but changes made to the consensus sequence affect the consensus and every constituent sequence in the contig. Note that the original sequence files stored on your computer will not be affected by these procedures.

To reassemble one or more contigs after editing them, see Reassemble contigs.

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