Ok, first of all thanks to you all for answering to me. Let me explain thoroughly my task:
I have a large database of records as I wrote before, in the form of:
NAME1
SEQUENCE1
NAME2
SEQUENCE2

[download]
etc. The NAME is usually 50-60 chars (small) but the SEQUENCE can be from 100 chars to maybe 2-3000 chars as you also pointed out.
What my script does (or I want it to do) is:
The user supplies an unknown query input, then I run a program called BLAST which tells me that this unknown input had 1,2,3....50...60...200 hits in my database. So, I know the NAME of each hit. My problem is that each time I need to look up the database file and retrieve the respective entries and then create a new file (let's say output file) which will have all NAME and SEQUENCE of the hits to process it further.
Plus my ultimate purpose it to create a webserver, so therefore this database file will be accessed quite frequently, that's why I am asking whether a database or a simple local search through a hash (at least that's what I can think about) is more recommended.

In reply to Re^2: Efficient way to handle huge number of records? by Anonymous Monk
in thread Efficient way to handle huge number of records? by Anonymous Monk

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