Since your goal is: "is to find small substrings within large DNA sequences". It is better than you look for the small substrings by dividing the entire genome into many bins of particular size, for example: if you have DNA sequence of 1 million characters then don't read the entire million character at once. You should

1. Bin1: read first 100 characters i.e. (character 0-99 taking into account that indexing in perl starts from 0) at once

2. look for the small substrings and

3. Bin 2: then again read the 1-100 characters and look for small substrings

4. Bin3: read 2-101 characters and so on until you have scanned the entire sequence.

In reply to Re: How to store large strings? by snape
in thread How to store large strings? by Anonymous Monk

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