in reply to Re^5: Exact string matching
in thread Exact string matching

Why? Why do you want to do this? What are you hoping to achieve by obtaining counts of repeats in this fashion? I completely understand what you want to do in the very limited context you have described. I have no idea at all why you want to do it, and it is that information that is most likely to get you a more practical solution - a solution to the bigger problem rather than a solution to a small part of it.

As an aside: how much RAM do you have in your computer and is it a 64 bit system? Are you using a 64 bit build of Perl? Both of these will have an influence on the solutions you may have available.

True laziness is hard work

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Re^7: Exact string matching
by saranrsm (Acolyte) on Oct 17, 2011 at 11:35 UTC

    "a solution to the bigger problem rather than a solution to a small part of it."

    Dear Monk, you are exactly correct. the reason for this work is to do with a biological context. In the context of DNA there are different types of repeat families (ya we do have families of repeats) such as tandem repeats are one type, where the repeats are in tandem eg) AATAAT,(AAT is repeated in tandem) next is palindromic repeat where a palindrome is repeated eg) AATTAAATCGACTAATTAA (AATTAA, a palindrome is repeated with some spacer in between)and so on..these repeats regions associates to various diseases and they also act as marker or as landmark to hunt down particular regions.(there are certain regions, that are flanked by certain repeat families)

    So if i have the informations such as the positions and the frequencies of the a particular repeat family, one could hunt down certain regions which are flanked by these repeats and with the number of frequencies of the certain repeats one could estimate how likely is this DNA (i.e. the string in our scripting context) mutated

    I hope i am clear this time, if not plz let me know

    system information RAM: 4 GB, Processor: Intel® Core™2 Quad CPU Q8300 @ 2.50GHz × 4, 64 bit machine, perl-v5.14.1 built for x86_64-linux, OS - Fedora 15

[reply]
      For repeated substrings and palindromes, you can extract the substrings to test further only from first half of the string. (Because, if it appears only in the second half, it is not repeated nor palindrome.)
[reply]

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