How can I find multiple motifs(substring) in a protein sequence(string)?

Question

The following script is for finding one motif in protein sequence.

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 \n\n";
      } else {
        print "not found \n\n";
    }
}
#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 \n\n";
}
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;
}

I am not sure how to extend this for finding multiple motifs (in a fixed order i.e motif1, motif2, motif3) in a given file containing a protein sequence.

Answer 1

You could simply use alternations (delimited by |) of the sequences. That way each sequence the regex engine can match it will.

/($h{4}D$x{4}D|$x{1,4}A{1,2}$s{2})/

Then you can test this match by looking at $1.