Combiming the patterns looks easy, And if you need to run diffence code for differnt patterns put them in a hash with the pattern as the key and the coderef as the value. 
use Regexp::Assemble;
my @search_patterns = ( 'CACGTG', 'GTGCAC' );

my $ra = Regexp::Assemble->new;
$ra->add( @search_patterns );

while ( $seq =~ /$ra/g ) {
  ...
}

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Boris

In reply to Re: Multiple Regex's on a Big Sequence by borisz
in thread Multiple Regex's on a Big Sequence by bernanke01

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