An iterative loop matching approach to the prediction of RNA secondary structures with pseudoknots

  • Ruan J
  • Stormo G
  • Zhang W
  • 9


    Mendeley users who have this article in their library.
  • 0


    Citations of this article.


In this paper we present a heuristic algorithm, iterative loop matching, for predicting RNA pseudoknots. The method can utilize either thermodynamic or comparative information or both, thus is able to predict for both aligned and individual sequences. Using 8-12 homologous sequences, the algorithm correctly identifies more than 90% of base-pairs for short sequences and 80% overall. It correctly predicts nearly all pseudoknots, while having very few false predictions. Comparisons show that our algorithm is more sensitive and more specific than existing methods. In addition, our algorithm is very efficient and can be applied to sequences up to several thousands of bases long.

Get free article suggestions today

Mendeley saves you time finding and organizing research

Sign up here
Already have an account ?Sign in

Find this document


Cite this document

Choose a citation style from the tabs below

Save time finding and organizing research with Mendeley

Sign up for free