as I told you further down you can use Tie::Hash to keep the interface functional.

IMHO there are no general solutions faster than storable ! *

You need to provide more infos.

If your php is calling your perlscript you should check if you can hold the data structure in memory.

You may also check if you're not running into RAM problems causing massive swappings.

I once speeded up a program just by trasforming a huge hash into a hash of hashes (by halving the keys). Since the system only retrieved the sub-hashes actually needed from disk swap, I had a fantastic speed gain.

If this is transferable to your case is unknown since you do not provide enough infos...

Footnote: (*)

from Storable

"SPEED
The heart of Storable is written in C for decent speed. Extra low-level optimizations have been made when manipulating perl internals, to sacrifice encapsulation for the benefit of greater speed."

This is how the hash basically looks (it goes on for about 6 million lines (genes)):

$VAR1 = {
          'microT' => {
                        'mmu-miR-704' => {
                                           'NM_009309' => '1',
                                           'NM_133983' => '1',
                                           'NM_175563' => '1',
                                           'NM_010889' => '1',
                                           'NM_008302' => '1',
                                           'NM_022023' => '1',
                                           'NM_009567' => '1',
                                           'NM_172938' => '1',
                                           'NM_029777' => '3',
                                           'NM_134189' => '1',
                                           'NM_175025' => '1',
                                           'NM_177327' => '1',
                                           'NM_026807' => '1',
                                           'NM_178779' => '3',
                                           'NM_010770' => '1',
                                           'NM_031998' => '1',
                                           'NM_145584' => '2',
                                           'NM_207682' => '1',
                                           'NM_001005525' => '1',
                                           'NM_080853' => '1',
                                           'NM_145519' => '1',
                                           'NM_031249' => '1',
                                           'NM_172923' => '1',
                                           'NM_001008700' => '1',
                                           'NM_198617' => '1',
                                           'NM_027400' => '1',
                                           'NM_026406' => '2',
                                           'NM_021296' => '2',
                                           'NM_027652' => '1',
                                           'NM_001045530' => '1',
                                           'NM_018830' => '1',
                                           'NM_025314' => '1',
                                           'NM_009041' => '1',
                                           'NM_026829' => '3',
                                           'NM_026618' => '1',
                                           'NM_027472' => '1',
                                           'NM_027870' => '1',
                                           'NM_001033239' => '1',
                                           'NM_026348' => '1',
                                           'NM_008223' => '1',
                                           'NM_009595' => '2',
                                           'NM_146094' => '1',
                                           'NM_144945' => '1',
                                           'NM_019510' => '1',
                                           'NM_001033251' => '1',
                                           'NM_001081213' => '3',
                                           'NM_008031' => '1',
                                           'NM_028719' => '1',
                                           'NM_133352' => '1',
                                           'NM_008133' => '1',
                                           'NM_008317' => '1',
                                           'NM_021327' => '1',
                                           'NM_178751' => '1',
                                           'NM_010260' => '1',
                                           'NM_025683' => '1',
                                           'NM_026383' => '1',
                                           'NM_001081367' => '1',
                                           'NM_001033354' => '2',
                                           'NM_026034' => '1',
                                           'NM_173395' => '1',
                                           'NM_010762' => '1',
                                           'NM_024432' => '1',
                                           'NM_175113' => '1',
                                           'NM_001077425' => '1',
                                           'NM_026374' => '1',
                                           'NM_026655' => '1',
                                           'NM_177345' => '1',
                                           'NM_027412' => '1',
                                           'NM_183187' => '1',
                                           'NM_016687' => '1',
                                           'NM_175640' => '1',
                                           'NM_007559' => '1',
                                           'NM_011269' => '1',
                                           'NM_010252' => '1',
                                           'NM_019657' => '1',
[download]

I'm not very familiar with Tie::Hash, so if you can give me a quick heads up on how I can use it to save time it would be great

you should benchmark if storable is really your bottleneck, starting a non persistent perl-process takes some time ...

The retrieval of the hash takes 12 seconds (out of less than 20 secs overall) so if I can take that number down a bit, I'm happy