#!/usr/bin/perl -w
use strict;
use DBI;

my $dbfile  = "./DNA.sqlite";

print "Creating new DNA Database\n";

if (-e $dbfile) {unlink $dbfile or die "Delete of $dbfile failed! $!\n";}

my $dbh = DBI->connect("dbi:SQLite:name=$dbfile","","",{RaiseError => 1})
    or die "Couldn't connect to database: " . DBI->errstr;

$dbh->do ("CREATE TABLE dna
             (  id        integer PRIMARY KEY AUTOINCREMENT,
                protein   varchar(10)   DEFAULT '',
                sequence  varchar(1000) DEFAULT ''
             );
          ");
          
          
$dbh->do('PRAGMA synchronous = 0');      # Non transaction safe!!!
$dbh->do('PRAGMA cache_size = 200000');  # 200 MB dynamic cache increase
                                         # makes index creation faster
$dbh->do("BEGIN");
import_data();
$dbh->do("COMMIT");  

$dbh->do("BEGIN"); 
$dbh->do ("CREATE INDEX iprotein_idx ON dna (protein)");     
$dbh->do("COMMIT");  


sub import_data
{
   my $add = $dbh->prepare("INSERT INTO dna ( protein, sequence)
                            VALUES(?,?)");
                               
   #...your loop to read the data goes here 
   # foreach protein and sequence...
   {
       $add->execute($protein, $sequence);
   }
   #  
}