EvryRNA : BiokoP

Secondary structure RNA prediction

Bi-objective programming pseudoknot Prediction

 

 

RNA structure prediction is an important field in Bioinformatics, and numerous methods and tools have been proposed. Pseudoknots are specific motifs of RNA secondary structures that are difficult to predict.

Almost all existing methods are based on a single model (thermodynamic or comparative) and return one solution, often missing the real structure. An alternative approach would be to combine different models and return a (small) set of solutions maximizing the probability that it contains the real structure.

Here we propose an original tool, BiokoP, for predicting optimal and sub-optimal RNA secondary structures with pseudoknots with one input sequence. It is based on a bi-objective integer programming algorithm allowing optimizing both energy and probabilistic criteria.

The executable BiokoP for Linux and the datasets are downloadable.

 


Pseudoknot dataset


Pseudoknot-free dataset


BiokoP for Linux

 

For any questions, comments or suggestions about BiokoP, please feel free to contact: fariza.tahi@ibisc.univ-evry.fr