my $fname = "file,fasta";
open my $fh, '<', $fname or die "Cannot open $fname, $!";

while (my $line = <$fh>) {

  chomp $line;



  if ($line =~ /CDECGKEFSQGAHLQTHQKVH/) {
    print "The protein contains the domain";
  } 
  else {
    print "The protein doesn't contain the domain";
  }
}