Text, lines and masking are meant to be used to annotate the multiple alignment. The TEXT command allows any piece of text to be located anywhere on the alignment. Clearly, however it makes little sense to superimpose the text over the alignment though this can be done! Accordingly, you must first make a space to put the text in. Usually, this will be a few lines below the multiple sequence alignment, but you may want to add text at the top, or somewhere in between two sequences. You can make space in two ways. Either by editing the block-file to introduce "dummy" sequences at the locations you want, or by making use of the ADD_SEQ command.
The ADD_SEQ command has two arguments, the sequence after which you want further sequences to be added, and how many blank sequences you need. Thus, we can reserve space for 5 lines of text underneath a 10 sequence multiple alignment with the following command.
ADD_SEQ 10 5
we can then put text below the alignment at the 20th residue.
TEXT 20 13 "Active Site His"
or any other position.
Similarly, we could draw a vertical line to point out which residue we mean
LINE LEFT 20 13 11
And change the font of the text to number 7 (whatever that has been set to):
FONT_RESIDUE 20 13 7
You can have multiple ADD_SEQ commands, but they must occur in sequence order. Thus:
ADD_SEQ 0 5 ADD_SEQ 5 12is legal. But
ADD_SEQ 5 12 ADD_SEQ 0 5
Is NOT!! NO CHECKING IS performed by the program for this error - so beware!
Note that add_seq commands refer to the actual sequence number as implied by the block file, not the number after applying the add_seq command. Thus, for a four sequence block file, if you want to add space for three sequences before sequence 1 and two sequences after sequence 3, the commands would be:
ADD_SEQ 0 3 ADD_SEQ 3 2
Text added with the TEXT command will not be split across page breaks, so you may in some circumstances need to fiddle a little with the location/pointsize for the text to get the desired result.
Masking is a technique for drawing irregular shaped outlines, or shaded regions - this should not be confused with the MASK family of commands described below. For example a histogram can be added to the bottom of an alignment by first defining some dummy sequences in the block-file that have letters building up the shape of the histogram, then using the SURROUND_CHARS or SHADE_CHARS commands together with the SUB_CHARS command to produce the desired effect. An example of this operation being used to show frequencies of secondary structure predictions is shown in example1.als and in the Protein Engineering paper.