The Bio::Grep module is pretty good as it provides a common interface for you to interact with several different fuzzy matchers, my favorite being Vmatch

agrep (i.e., approximate grep) is a nice tool for this sort of thing. it's not a standard LINUX tool, but it is a good one.

Here's one implementation: ftp://ftp.cs.arizona.edu/agrep/

from the README at the above URL:

" ...for example, "agrep -2 homogenos foo" will find homogeneous as well as any other word that can be obtained from homogenos with at most 2 substitutions, insertions, or deletions. "

You are looking for a fuzzy pattern matching program, try perl module String::Approx:

"Perl extension for approximate matching (fuzzy matching)"

For fuzzy pattern matching excercise and scripts go through VCU bioinformatics notes on pattern matching

Just assigning a regexp to a scalar will not work in perl for sub-sequence pattern matches e.g.

$searchSeq = "AAA[TA]";

Instead you need to use quote regular expression (qr) operator

$searchSeq = qr/AAA[TA]/;