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[Seqan-dev] Suffix links

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  • From: John Reid <j.reid@mail.cryst.bbk.ac.uk>
  • To: "seqan-dev@lists.fu-berlin.de" <seqan-dev@lists.fu-berlin.de>
  • Date: Fri, 31 May 2013 19:38:58 +0100
  • Reply-to: SeqAn Development <seqan-dev@lists.fu-berlin.de>
  • Subject: [Seqan-dev] Suffix links

Hi,

I had a little google for this but I didn't find the answer. I have an
algorithm which should run quickly on a suffix tree or array. However in
the algorithm I will need to move from a node for say the suffix GCCGAA
to the node for CCGAA. This is obviously expensive in a normal suffix
tree. However I think that some suffix tree construction algorithms
create suffix links (perhaps Ukkonen's algorithm) that do exactly this.
Does SeqAn contain such algorithms and how can I access the suffix links
after construction?

Thanks,
John.



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