Your are focusing too much on memory consumption or architecture as correlating with runtime speed. That is almost never the case.
As Giovanni M Dall'Olio stated a few times the key to doing anything faster is to run more of them at the same time. If your computer has more cores (almost all do) then chop the data in more pieces, run the search on each piece separately. Your jobs still complete in N amount of time but more pieces are done in the same amount of time.
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Istvan Albert
I don't know much about technical aspects of computers but I think 64bit programmes can use more memory than 32bit ones. The limit for 32bit is 4GB - if you have more RAM than that, you should benefit from 64bit version.
I have 96674MB of memory and 98292MB of Swap. So it will reduce the time of analysis?
Yes, the 64bit version will allow you to use all the RAM and probably be faster (http://drive5.com/usearch/manual/bitness.html). However 5 hours is not a long time for an analysis, it's up to you to decide whether it is worth. You may even try running the jobs in parallel.
I know it's not very long but I need to do it faster just for one analysis (required delivery time is very short) and I am looking for fast solutions. Thank you ! :)
What about running it in parallel?