MSA: Modifying and deleting sequences

Before editing, you need to unlock the sequences by clicking the padlock button to display an open padlock. If you try to edit a locked sequence, you will be asked if you want to unlock the file.

TO MOVE a selection within a sequence

1. Do one of the following:

- place the cursor over the selection until the cursor symbol changes to a hand, then drag the selection to a new location

- use the cursor keys to move the selection to the left or right.

NOTE: A selection can only be moved within the gaps between it and the rest of the sequence. If there are no gaps around the selection, it cannot be moved, and the cursor symbol will not change to a hand.

INSERTING RESIDUES

When you type or paste residues, they are inserted into the sequence. At the end of the sequence, gaps are truncated to keep the alignment length constant. If there are no gaps at the end of the sequence, gaps are appended to all the other sequences in the alignment to keep them

the same length.

TO INSERT and remove gaps in a sequence

1. Position the cursor where you want to add or remove a gap.

2. Do one of the following:

- to insert gaps, use the spacebar

- to remove gaps, use the backspace key.

TO INSERT residues by typing

1. Position the cursor where you want to add the residues.

2. Type the residues, using the keyboard or programmed numeric keypad.

TO PASTE residues into a sequence

1. Position the cursor where you want to add the residues.

2. Use Edit | Paste to insert the residues from the clipboard.

NOTE: If you paste a block of residues from more than one sequence into the alignment, they are always inserted as new sequences, with names based on their parent sequences. You cannot insert residues into more than one sequence at a time.

During alignment, it may be necessary to insert one or more gaps in an entire block of sequences:

TO INSERT gaps in multiple sequences

1. Select a block of residues immediately after the position where the gap should be.

2. Press any "gap" key (space, hyphen, or period).

A gap will be inserted in front of the selected block, in all the selected sequences. Repeat as required.

DELETING AND REPLACING residues

TO DELETE residues in a sequence

1. Select the residues you want to delete. You can select a block of residues from more than one sequence.

2. Choose Edit | Cut to delete the residues.

To keep all sequences the same length, gaps are appended to the affected sequences as required.

You can also use the delete key to delete residues.

TO REPLACE or clear residues in a sequence

1. Select the residues you want to replace.

2. Do one of the following:

- Choose Edit | Clear to replace all the residues by gaps

- Type or paste in the new residues.

NOTE: You cannot use a block of residues from more than one sequence to replace another selected block. You must insert residues into one sequence at a time.

TO DELETE sequences

1. Select the name of a sequence you want to delete. To select more than one sequence, hold down the Shift key and click on the required names.

2. Choose Edit | Delete Sequence to delete the sequences.

Alternatively, use the Cut function; the sequences will be placed on the Clipboard.