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my ( $R_score, @protein, @R_score_protein );

my ( @protein, @R_score_protein );
...
push( @R_score_protein, $1 );

use Getopt::Long;
our URL = "http://www.bork.embl-heidelberg.de/g2d/"
...
GetOptions( 'url=s', \$URL ) || die ( "Error reading command line args
+" );
my $browser = LWP::UserAgent->new();
my $resp = $browser->get( $URL );

while ( $content_all =~ m{R\-score<\/A>\s=\s(\d\.\d+)\;}g ) {
    push( @R_score_protein, $1 );
...
while ( $content_all =~ m{\[(NP_\d+)\]}g ) {
    push @protein, $1;
}

my $protein_re = qr|\[(NP_\d+)\]|;
my $score_re = qr|R-score</A>\s=\s(\d\.\d+)|;
while ( $content_all =~ m{$protein_re} ) .....
while ( $content_all =~ m{$score_re} ) ....

# $record stores references to hashes, 
# which are accumulated in @records
...
        push( @{ $record->{'score'} }, $score );
    }
}

for my $records ( @records ) {
    print "Proteins: ", join( ", ", @{ $record->{'protein'} } ), "\n" 
...
    print "Score: ", $record->{'score'}, "\n";
    print "-" x 72;
}