Stem-loop Structure Search

##article.authors##

  • Simone Scalabrin
  • Alberto Policriti
  • Michele Morgante

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https://doi.org/10.1685/

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The base-pairing of a nucleic acid secondary structure is a sort of biological palindrome. The base pairs of nucleic acid stems nest in a palindromic fashion with complementary base pairings rather than identical letters. In addition, nucleic acid stems are usually separated by a loop, i.e. a non palindromic sequence. At the moment, the problem of finding such a structure is solved through dynamic programming or in linear time with the use of the lowest common ancestor (S2_ScalabrinPolicriti0.png) preprocessing. We propose an algorithm which exploits matching statistics, is linear on the size of the input S2_ScalabrinPolicriti1.png, does not use S2_ScalabrinPolicriti0.png, builds the suffix tree only for S2_ScalabrinPolicriti1.png and saves a lot of memory. [DOI: 10.1685/CSC06137] About DOI

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2007-10-01

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##issue.vol## 1 (2006)

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Articles

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