find the longest orf in an aa seq.

gistfile1.pl

#!/usr/bin/perl
my $p = 'AAMAAT-ATAMAAAT-AT'; #example protein
my @l = find_orfs($p);        #calls subfunction
my ($longest, $longest_aa) = longest_orf($p, @l); #calls subfunction
print "protein = $longest_aa longest = $longest\n";

sub find_orfs ($protein) {
  my ($protein) = @_;
  print "protein $protein\n";
  my $len = length ($protein);
  my $aa;
  my $new_aa;
  for( $i=0; $i < $len; $i++) {
    $aa = substr($protein, $i, 1); #look at single aa
    if ($aa eq 'M') {              #start aa
      for( $j=$i+1; $j < $len; $j++) {
        $new_aa = substr($protein, $j, 1);  #searches after the start aa
        if($new_aa eq '-') {   
          $locations[$i][$j] = $j - $i;     #records length of orf found
          last;
        } else {
          $locations[$i][$j] = 0;
        }
      }
    }
  }
  return (@locations);
}

sub longest_orf { #find longest orf in list of orfs
  my ($protein, @locations) = @_;
  my $longest = 0;
  my $longest_aa = '';
  my $len = length($protein);
  for( $i=0; $i < $len; $i++) {
    for( $j=0; $j< $len; $j++) {
      if ($longest < $locations[$i][$j]) { #current longest orf is longer than longest orf so far
        $longest = $locations[$i][$j]; #records length
        $longest_aa = substr($protein, $i, $longest); #records aa
      }
    }
  }
  return ($longest, $longest_aa);
}

updated to be functions instead of 1 giant script