perl – 如何在蛋白质序列(string)中找到多个motifs(substring)

use strict;
use warnings;

my @file_data=();
my $protein_seq='';
my $h= '[VLIM]';   
my $s= '[AG]';
my $x= '[ARNDCEQGHILKMFPSTWYV]';
my $regexp = "($h){4}D($x){4}D"; #motif to be searched is hhhhDxxxxD
my @locations=();

@file_data= get_file_data("seq.txt");

$protein_seq= extract_sequence(@file_data); 

#searching for a motif hhhhDxxxxD in each protein sequence in the give file

foreach my $line(@file_data){
    if ($motif=~ /$regexp/){
        print "found motif nn";
      } else {
        print "not found nn";
    }
}
#recording the location/position of motif to be outputed

@locations= match_position($regexp,$seq);
if (@locations){ 
    print "Searching for motifs $regexp n";
    print "Catalytic site is at location:n";
  } else {
    print "motif not found nn";
}
exit;

sub get_file_data{
    my ($filename)=@_;
    use strict;
    use warnings;
    my $sequence='';

    foreach my $line(@fasta_file_data){
        if ($line=~ /^s*(#.*)?|^>/{
            next;
          } 
        else {
            $sequence.=$line;
        }
    }
    $sequence=~ s/s//g;
    return $sequence;
}

sub(match_positions) {
    my ($regexp,$sequence)=@_;
    use strict;
    my @position=();
    while ($sequence=~ /$regexp/ig){
        push (@position,$-[0]);
    }
    return @position;
}

我不知道如何扩展这个以在含有蛋白质序列的给定文件中找到多个基序(以固定顺序,即motif1,motif2,motif3).