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Re^2: finding longest common substring

by monkfan (Curate)
on Nov 24, 2005 at 01:55 UTC ( #511302=note: print w/replies, xml ) Need Help??


in reply to Re: finding longest common substring
in thread finding longest common substring

Hi,
I was referred to your node above from my earlier request about Generalized Suffix Tree.
Since I am very interested to the use of it for bioinformatics purpose.

I just want to clarify:
  • Does you implementation above covers the "generalized" suffix tree?
    Or is it the same with S.Yona's module?
  • If so, do you have a CPAN module for it?
  • Otherwise, I would really appreciate if you can kindly point me where can I find the actual Perl implementation for it, if you happen to know one.

Thanks so much beforehand.
Hope to hear from you again.

Regards,
Edward

Replies are listed 'Best First'.
Re^3: finding longest common substring
by thospel (Hermit) on Dec 03, 2005 at 17:36 UTC
    No, it's not a generalized suffix tree. What I implemented here is basically the suffixtree of the concatenation of the strings, which has the same sort of space and time complexity for operations as a generalized suffix tree.

    Note that I don't expect that a pure perl version of suffix trees will be very usable for huge strings since the memory overhead of the datastructures will just be too much. This stuff needs an XS module.

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