SQLite is a database, and you need to define indexes for columns that you will be selecting. (You may want to read a good database book for examples of when, and when NOT to use an index... for that matter, when you want to use a database and when to use a delimited text file...) Adding an index improves performace, at least at select time. Not tested for replace time, but I leave that as an exercise to the user...
Example code:

#!/usr/local/bin/perl
use strict;
use DBI;
use DBD::SQLite;
use Benchmark;
my $dbh = DBI->connect("dbi:SQLite:dbname=testdb","","");

print "Connected to Database OK.\n";
print "Creating Tables && INSERTING\n";

my $sql = qq{CREATE TABLE A (A INT, B VAL)};
my $sth = $dbh->prepare($sql);
$sth->execute();

my $i=0;
while ($i<10000){
  my $sql = qq{INSERT INTO A(A,B) VALUES (?,?)};
  my $sth = $dbh->prepare($sql);
  $sth->execute($i,$i);
  $i++;
}
print "DONE\n";


sub doSelect{
  # Yes, I could pre cache the query, but this won't affect the result
+s
  my $sql = qq{SELECT A FROM A WHERE B = ?};
  my $sth = $dbh->prepare($sql);
  my $i =int( rand 10000);
  
  $sth->execute($i);
  my @ary = $sth->fetchrow_array();
}
timethese (10000,{'MethodOne'=>'&doSelect'});

my $sql2 = qq{CREATE INDEX FOO ON A(B)};
my $sth2 = $dbh->prepare($sql2);
$sth2->execute();

timethese (10000,{'MethodOne'=>'&doSelect'});
[download]

Results:

Connected to Database OK.
Creating Tables && INSERTING
DONE
Benchmark: timing 10000 iterations of MethodOne...
 MethodOne: 100 wallclock secs (71.48 usr + 18.18 sys = 89.66 CPU) @ 1
+11.53/s (n=10000)
Benchmark: timing 10000 iterations of MethodOne...
 MethodOne:  5 wallclock secs ( 2.83 usr +  1.11 sys =  3.94 CPU) @ 25
+38.07/s (n=10000)
[download]

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