1.24.5 Editing Alignment Sequences

  • The DNA template sequence in a project with alignments can be edited as usual, however the ClustalW alignment will not be re-run.

Editing the Alignment Sequences

  • Aligned sequences can only be edited via right click menus in the following ways:

    • If an addition exists in the aligned sequence, either select “Add to template” or “Delete from alignment” (Figure 1.24.5.1).

    Figure 1.24.5.1: Addition in alignment.

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    • If a gap exists in the aligned sequence, either select “Add from template” or “Delete from template” (Figure 1.24.5.2).

    Figure 1.24.5.2: Gap in alignment.

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    • If a mismatch exists, either select “Copy from template” or “Replace in template” (Figure 1.24.5.3).

    Figure 1.24.5.3: Mismatch in aligment.

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    • If a mismatch exists in terms of an ambiguous base (N) in the alignment, either select “Copy from template” or “Replace to A, T, G or C” (Figure 1.24.5.4).

    Figure 1.24.5.4: Ambiguous Base.

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Manual Trimming (coming soon)

  • Sequences can be manually trimmed using the right click drop down menu:

    • Trim to.. “Selection” inverts the selection and dulls out the sequence surrounding the selection
    • Trim to..”Start” trims and dulls out the sequence up to the left of the caret
    • Trim to..”End” trims and dulls out sequence up to the right of the caret
  • Once the sequence has been trimmed there is a trimming caret which can be dragged back and forth to trim the sequence manually.

  • If the sequence is on the reverse strand then trimming options work in the reverse.