While sequences such as full-length calmodulin proteins typically align well throughout the entire length of the polypeptides, full-length alignments of other sequences may not generate such neat blocks of similarity. For example, multiple sequence alignments of full-length beta-tubulins typically show “ragged” carboxyl termini, where the different tubulins terminate at varying positions with respect to the consensus. The “ragged” termini are caused by considerable length variance of the beta tubulins and carboxyl termini that are poorly conserved. Therefore, once you have performed an initial multiple alignment for two or more sequences, you may wish to realign a section using different parameters or a different alignment engine.

To perform a sequence subalignment:

  1. Make a single selection across the aligned sequences. One way to do this is to drag the mouse along the consensus sequences. Another is to triple-click on a feature. Either selects a “vertical slice” of all the sequences in the current alignment. If you plan to use Mauve as the alignment algorithm, note that you can only select and subalign sequences within the active block.
  1. Choose Align > Realign Subsequences to open a dialog populated for a sequence subalignment.
  1. Choose the desired alignment method from the drop-down menu, then set other options as desired.

  1. Press Align.
  • Occasionally, the new subalignment may no longer be the same as the optimal alignment your alignment method would generate from scratch for this particular set of sequence coordinates. You may want to realign the shorter sequences to evaluate this possibility.
  • If you are not sure exactly which segment of an alignment you need for your new alignment, you may select the region liberally, generate the new alignment, and continue to select sub-regions of the alignment until you are satisfied.
  • You can create a new alignment from a selection of any length, but you cannot create a new alignment from discontiguous segments of your current alignment.

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