This is my current working code. Its purpose is to find a string of amino acids that match a regular expression and put the matching string as well as what is found before and after the matching string in 3 separate scalars. 
if($sequence[1] =~ m/^(.*)$reg(.*)$/i){
          $aligned[$posCount][0] = $1;
          $aligned[$posCount][1] = $2;
          $aligned[$posCount][2] = $3;
}

[download]
$reg used to be a regular expression contained in a single set of parens. Example:  $reg = (K[STN]\w\w[GST]\w{1,2}[KRA]R[IVF]); But now I have set it up to automatically place parens around \w of variable length, so the previous $reg would now be:  $reg = (K[STN]\w\w[GST])(\w{1,2})([KRA]R[IVF]); Such that a string searched against a regular expression with 1 variable length component would be split into 5 pieces. The stuff found before the match, constant length match1, variable length match, constant length match2, the stuff found after the match. I want to make it so a user could have any number of variable length regions. Is there a method with which I could add recursion? 
if($sequence[1] =~ m/^(.*)$reg(.*)$/i){
         for(my $x = 0; $x < $numInsertionDeletes; $x++){
               $aligned[$posCount][$x] = ????????;
         }
      }

[download]

In reply to Need a Method to add recursion to my regex by vivomancer

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