EvryRNA : BiokoP
Secondary structure RNA prediction
Secondary structure RNA prediction
Bi-objective integer programming for
RNA secondary structure prediction
with pseudoknots
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 standalone version of BiokoP (for Linux) is available following the link below:
Datasets used in the paper are available following links below: