use Text::Ngram qw( ngram_counts );
use ...
use ...

my $db = "/home/db/repository/megalith.db";
my $ngram_width = 5;
my %protein_search_hash;

unlink $db;
tie %protein_search_hash, 'MLDBM', -Filename => $db, 
                                   -Flags    => DB_CREATE | DB_INIT_LOCK
         or die "Cannot open database '$db: $!\n";

open FILE, "<test_data_2MB.txt" 
    or die "Failed to load test_data: $!\n";
my $fasta_sequence = do { local $/; <FILE> };
close(FILE);

# Precompile regex for speed
my $regex = qr/>([\S]*)\s*.*\s([A-Za-z\s]+)/;
my $regex_d = qr/^>[\S]*\s*.*\s[A-Za-z\s]+/;

# PARSE $fasta_sequence and split header from the sequence
while( $fasta_sequence =~ m/$regex/igm ) {
    my $sequence = $2;
    my $header = $1;
    $sequence =~ tr/[\r|\n]//d; # delete all line breaks
    # generate n-grams
    my $ngram_href= ngram_counts($sequence, $ngram_width);
    $protein_search_hash{$header} = $ngram_href;
}
...
...
...

##</code><code>##

    $protein_search_hash{$header} = $ngram_href;

##</code><code>##

    my $ngram_href= ngram_counts($sequence, $ngram_width);