Keyboard Edits

This continues on from the previous exercise, and recreates the final part of the example ferredoxin alignment from the unaligned sequences using Jalview’s keyboard editing mode.

Window users: Please only use [SHIFT]-[SPACE] in this exercise.

Mac users: [CTRL]-[SPACE] can also be used instead of [SHIFT]-[SPACE].

  1. Load the sequence alignment at, or con- tinue using the edited alignment. If you continue from the previous exercise, first right click on the sequence ID panel and select Reveal All. Enter cursor mode by pressing [F2] (or [Fn]-[F2] (Mac)).

  2. Insert 58 gaps at the start of the sequence 1 (FER_CAPAA). Press 58 then [SPACE].

  3. Go down one sequence and select rows 2-5 as a block. Click on the second sequence ID (FER_CAPAN). Hold down shift and click on the fifth (FER1_PEA).

  4. Insert 6 gaps at the start of this group. Go to column 1 row 2 by typing 1,2 then press [RETURN]. Now insert 6 gaps in all the sequences. Type 6 then hold down [SHIFT] and press [SPACE].

  5. Now insert one gap at column 34 and another at 38. Insert 3 gaps at 47. Press 34C then [SHIFT]-[SPACE]. Press 38C then [SHIFT]-[SPACE]. Press 47C then 3 [SHIFT- SPACE] the first through fourth sequences are now aligned.

  6. The fifth sequence (FER1_PEA) is poorly aligned. We will delete some gaps and add some new ones. Press [ESC] to clear the selection. Navigate to the start of sequence 5 and delete 3 gaps. Press 1,5 [RETURN] then 3 [BACKSPACE] to delete three gaps. Go to column 31 and delete the gap. Press 31C [BACKSPACE] .

  7. Similarly delete the gap now at column 34, then insert two gaps at column 38. Press 34C [BACKSPACE] 38C 2 [SPACE]. Delete three gaps at column 44 and insert one at column 47 by pressing 44C 3 [BACKSPACE] 47C [SPACE]. The top five sequences are now aligned.

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