Thanks, You're solution helped quite a bit. The dashes in the example are meant to be there to show missing data in the files.

Ok, so check this solution with dashes, in the case you need them; if not, use the previous snippet.

#!/usr/bin/perl

use strict;
use warnings;

# Constants
my $BLANK_LINE = qr/^\s+$/;
my $KEY = qr/>([A-Z])/;

# Variables
my %content = ( 'A' => [], 'B' => [], 'C' => [], 'D' => [], 'E' => [],
                'F' => [], 'G' => [], 'H' => [], 'I' => [], 'J' => [],
                'K' => [], 'L' => [], 'M' => [], 'N' => [], 'O' => [],
                'P' => [], 'Q' => [], 'R' => [], 'S' => [], 'T' => [],
                'U' => [], 'V' => [], 'W' => [], 'X' => [], 'Y' => [],
                'Z' => [] );

# Take the data
for (<*.db>) {
    open(FILEDB, $_) or die "No se puede abrir el archivo $_: $!\n";
 
    my $key;
    my %contentTemp;
                        
    for (<FILEDB>) {
        if (/$BLANK_LINE/) {
            next;
        } elsif (/$KEY/) {
            $key = $1;
            $contentTemp{$key} = [];
        } else {
            chomp;
            push(@{$contentTemp{$key}}, $_);
        }
    }

    # Are there some missing keys?
    foreach my $k (sort keys %content) {
        if ($contentTemp{$k}) {
            push(@{$content{$k}}, @{$contentTemp{$k}});
        } else {
            push(@{$content{$k}}, "-, -");
        }
    }

    close(FILEDB);
}

# Write the new file
open(FILEDB, ">resultado.db") or die "No se puede abrir el archivo res
+ultado.db: $!\n";

for my $key (sort keys %content) {
    print FILEDB ">$key\n\n" . join(", ", @{$content{$key}}) . "\n\n";
}

close(FILEDB);
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