Sequence Window : Edit Commands
Enable editor
Turns on the editor, allowing you to change the alignment.
Undo
Undo the latest operation; Ctrl+Z has the same effect as this menu item. All operations
(the items under this Edit menu) that change the alignment are undoable.
Redo
Redo the last operation undone (Shift+Ctrl+Z).
Split block
To split an aligned block, select this item then move the mouse over the block
to be split and click once. The block under the mouse will be split such that
the new (rightmost) block will start at the column under the mouse.
Merge block
To merge two or more adjacent aligned blocks, select this item then click and
drag the mouse across the blocks to be merged. These blocks will then be joined
into a single large block.
Create block
To create a new block, select this item then click and drag the mouse across columns
of unaligned residues where you would like a new block to be created. Note that
all columns of the alignment in the selected area must contain residues (no unaligned
gaps).
Delete block
To delete a block, select this item and then click on any aligned block. That
block will be removed and the residues marked unaligned.
Sync structure colors
Always sync structure colors
Because the alignments are color-coded, changes to the alignment can cause changes
in color of structures in the alignment. By default, Always sync structure
colors is on, which means this redrawing of structures will take place automatically.
This can be turned off for slower computers where redraws take a long time; use
Sync structure colors to manually redraw the structures with any new colors.
Sort rows
Use this item to sort all but the first row of the current alignment. The algorithms
available for sorting are:
- By identifier: sort so
that all PDB identifiers are at the top of the list in alphabetical order,
followed by all non-PDB's sorted by numerical order for gi's or alphabetical
order for accessions.
- By score: sort by
PSSM+contact score. You will be prompted for a weight between these two, then
rows will be sorted with the highest scoring rows at the top. The scores will
also be displayed in the status line when you move the mouse over each
sequence.
- Float PDBs: simply moves
all PDB sequences to the top of the alignment, but without otherwise changing
the relative ordering of the PDB sequence or non-structured rows.
- Float highlights: floats any sequences that contain highlights
to the top of the alignment.
- Float geometry violations: floats any sequences that contain
geometry vioaltions.
- Self-hit: sorts by BLAST score between each sequence and the PSSM
constructed from the current alignment.
- Proximity sort: select this menu item and then click on any but the
first row to do a proximity sort. This will move the selected sequence
to a position in the alignment according to its relative sequence conservation
with the first row. Then the other sequences most similar to the selected
row will be clustered around it. This is useful for grouping similar sequences
together, and for automatically finding similar sequences in a large alignment.
- By loop length: select anyplace in an unaligned region, and this will
sort the sequences according to the number of residues in that region (highest
first).
Delete row
Select this item and then click on any but the first sequence to remove that
row from the alignment.
Alignment refiner
The refiner algorithm is documented in a separate page. See also Chakrabarti S. et. al., Nucleic Acids Res. 2006 May 17, 34(9):2598-606
(PMID 16707662).