The simple answer to is there a way to tell the RE engine to ignore newline characters is No.

However, I think that you are dismissing the idea of generating the regex too quickly. It is a quite legitimate thing to do. In this case I would use \s* instead of \n* if the is any chance of other whitespace that you want to ignore.

#! perl -slw
use strict;

my $search_string = 'uekasdh';

# Split the search string into chars and intersperse
# them with the "ignore whitespace" regex.
my $re =  join '\s*', split '', $search_string;

my $data = do{ local $/; <DATA> }; # Slurp the data
$data =~ s[$re][jjjjjjjj];         # Find and replace.

print $data;
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