LiCoRNA: aLignment of Complex RNAs

A tool for structure sequence alignment


Our News

17 Apr 2017
LiCoRNA v1.0 is released
The first version of LiCoRNA contains three main programs: alignerDP, alignerSB, alignerMEA. You could download here





LiCoRNA is a software for structure sequence alignment for two RNAs in the presence of arbitrary pseudoknots. The program is based on the tree decomposition of query sequence and a general parameterized algorithm to compute the optimal alignment.


Main programs

Now LiCoRNA mainly has three different programs:

  • alignerDP (Dynamic Programming): the general dynamic programming algorithm to compute the optimal alignmnet. Besides we could also get the k-suboptimal alignment.
  • alignerSB (Stochastic Backtrack): generate a representative sample of alignment using stochastic sampling.
  • alignerMEA (Maximum Expected sequence-structure alignment): compute an alignment with maximum expected accuracy over all alignments that are sampled by stochastic sampling.


Related Publications

If you find LiCoRNA useful to your research, please contribute to its continued development by citing its supporting manuscript:

Rinaudo P, Ponty Y, Barth D, et al. Tree decomposition and parameterized algorithms for RNA structure-sequence alignment including tertiary interactions and pseudoknots[C]//International Workshop on Algorithms in Bioinformatics. Springer Berlin Heidelberg, 2012: 149-164.


processing paper



LiCoRNA is being developped as a collaboration work by Wei Wang, Yann Ponty, Philippe Rinaudo, Mathieu Barba, Alain Denise.

The basic theoretical aspects are from the paper of Philippe Rinaudo et al.

Mathieu Barba contributes the codes for tree decomposition of the query sequence in JAVA.

Wei Wang, Yann Ponty, Philippe Rinaudo contributes the codes for Dynamic Programming, Stochastic Backtracking and suboptimal alignment in C++.

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