IPknot: fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming.
Kengo SatoYuki KatoMichiaki HamadaTatsuya AkutsuKiyoshi AsaiPublished in: Bioinform. (2011)
Keyphrases
- integer programming
- rna secondary structure prediction
- rna secondary structures
- rna sequences
- secondary structure
- np hard
- stochastic context free grammars
- edit distance
- linear programming
- constraint programming
- rna structures
- cutting plane algorithm
- column generation
- computational methods
- integer program
- protein sequences
- dna sequences
- constraint satisfaction problems
- graphical models
- hidden markov models
- optimal solution