maskseq allows you to mask off regions of a sequence with a specified letter.

To mask off bases 10 to 12 from a sequence gatta.seq and write to the new sequence file gatta2.seq:

% maskseq gatta.seq gatta2.seq -reg=10-12

To mask off bases 20 to 30 from a sequence hdh.seq using the character n and write to the new sequence file hdh2.seq:

% maskseq hdh.seq hdh2.seq -reg=20-30 -mask=n

To mask off the regions 20 to 23, 34 to 45 and 88 to 90 in yuy.seq:

% maskseq yuy.seq yuy2.seq -reg=20-23,34-45,88-90

Mandatory qualifiers:

[-sequence] (sequence)

Sequence USA.

-regions (range)

Regions to mask. A set of regions is specified by a set of pairs of positions. The positions are integers. They are separated by any non-digit, non-alpha character. Examples of region specifications are: 24-45, 56-78, 1:45, 67=99, 765..888, and 1,5,8,10,23,45,57,99.

[-outseq] (seqout)

Output sequence USA.

Optional qualifiers:

-maskchar (string)

Character to use when masking. Default is X for protein sequences, and N for nucleic sequences.