Multiple Sequence Alignment

  1. Close all windows using Window $\Rightarrow$ Close All.

  2. Open an alignment by selecting File $\Rightarrow$ Input Alignment $\Rightarrow$ From URL from the Jalview desktop window and enter and click OK.

  3. Select Web Service $\Rightarrow$ Alignment $\Rightarrow$ Muscle with Defaults in the alignment menu. A window opens giving the job status. After a moment, a new window opens with the sequences aligned.

  4. Return to the original alignment, and align the sequences using Clustal Omega

  5. by selecting the Web Service $\Rightarrow$ Alignment $\Rightarrow$ ClustalO $\Rightarrow$ with Defaults.

  6. Compare the two results and you should notice small differences in their alignments especially at the start. Opening and enlarging the overview window might help (using View $\Rightarrow$ Overview Window).

  7. In the ClustalO alignment (identified from the title panel), hide columns 60-125 by clicking and dragging the mouse in the alignment ruler, right-click and select Hide Columns in the context menu.

  8. Select Web Service $\Rightarrow$ Alignment $\Rightarrow$ Mafft with Defaults to submit the visible portion of the alignment to MAFFT. When the web service job pane appears, note that there are two job status panes shown. When the MAFFT alignment has finished, compare the alignment of the N-terminal visible region in the result with the corresponding region of the original alignment.

For more information on this topic go to section 5.1 of the Jalview manual.
 This exercise can be viewed in the Multiple Sequence Alignment and Analysis video.