### Editing Alignments

You are going to manually reconstruct part of the example Jalview alignment available at https://www.jalview.org/examples/exampleFile.jvp. Mac Users: Please use the Apple or [CMD] key in place of [CTRL] for key combinations such as [CTRL]-A.

Remember to use [CTRL]-Z to undo an edit, or the File $\Rightarrow$ Reload function to revert the alignment back to the original version if you want to start again.

1. Load the URL https://www.jalview.org/tutorial/unaligned.fa which contains part of the ferredoxin alignment from PF03460.

2. Select the first 7 sequences, and press H key to hide them (or right click on the sequence IDs to open the sequence ID context menu, and select Hide Sequences).

3. Select FER3_RAPSA and FER_BRANA. Slide the sequences to the right so the initial residue A lies at column 57 using the → key.

4. Select FER1_SPIOL, FER1_ARATH, FER2_ARATH, Q93Z60_ARATH and O80429_MAIZE

Hint: you can do this by pressing [CTRL]-I to invert the sequence selection and then deselect FER1_MAIZE), and use the → key to slide them to so they begin at column 5 of the alignment view.

1. Select all the visible sequences (those not hidden) in the block by pressing [CTRL]-A. Insert a single gap in all selected sequences at column 38 of the alignment by holding [CTRL] and clicking on the residue R at column 38 in the FER1_SPIOL, then drag one column to right. Insert another gap at column 47 in all sequences in the same way.

2. Correct the ferredoxin domain alignment for FER1_SPIOL by inserting two addi- tional gaps after the gap at column 47. First press [ESC] to clear the selection, then hold [SHIFT] and click and drag on the G and move it two columns to the right.

3. Now complete the alignment of FER1_SPIOL with a locked edit by pressing [ESC] and select columns 47 to 57 of the FER1_SPIOL row. Move the mouse onto the G at column 50, hold [SHIFT] and drag the G in column 47 of FER1_SPIOL to the left by one column to insert a gap at column 57.

4. In the next two steps you will complete the alignment of the last two sequences. Select the last two sequences (FER1_MAIZE and O80429_MAIZE), then press [SHIFT] and click and drag the initial methionine of O80429_MAIZE 5 columns to the right so it lies at column 10. Keep holding [SHIFT] and click and drag to insert another gap at the proline at column 25 (25C in cursor mode). Remove the gap at column 44, and insert 4 gaps at column 47 (after AAPM).

5. Hold [SHIFT] and drag the I at column 39 of FER1_MAIZE 2 columns to the right. Remove the gap at FER1_MAIZE column 49 by [SHIFT]-click and drag left by one col- umn. Press [ESC] to clear the selection, and then insert three gaps in FER1_MAIZE at column 47 by holding [SHIFT] and click and drag the S in FER1_MAIZE to the right by three columns. Finally, remove the gap in O80429_MAIZE at column 56 us- ing [SHIFT]-drag to the left on 56C.

6. Use the Edit $\Rightarrow$ Undo Edit and Edit $\Rightarrow$ Redo Edit menu option, or their keyboard shortcuts ([CTRL]-Z and [CTRL]-Y) to step backwards and replay the edits you have made.

For more information on this topic go to section.2.6 of the Jalview manual.