Creating an SQLite DB is not that hard. I haven't tested this code, but this is at least the general idea. 
#!/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 increa
+se
                                         # 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);
   }
   #  
}

[download]
Update:
Basically when creating the DB, you want to turn all the ACID stuff off.
That means: don't wait for writes to complete, don't do complete transactions for each "add", run the cache size up from default of 20MB to at least 200 MB for more efficient index creation. Run as "lean and mean" as you can.

In reply to Re^3: Efficient way to handle huge number of records? by Marshall
in thread Efficient way to handle huge number of records? by Anonymous Monk

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