IPknot for predicting RNA pseudoknot structures using integer programming

Requirements

• Vienna RNA package (>= 1.8)
• GNU Linear Programming Kit (>=4.41) or Gurobi Optimizer (>=2.0) or ILOG CPLEX (>=12.0)

Install

For GLPK,

./configure --with-vienna-rna=/path/to/vienna-rna --with-glpk

For Gurobi,

./configure --with-vienna-rna=/path/to/vienna-rna --with-gurobi=/path/to/gurobi

For CPLEX,

./configure --with-vienna-rna=/path/to/vienna-rna --with-cplex \
            --with-cplex-include=/path/to/cplex/include \
	        --with-cplex-lib=/path/to/cplex/lib

Usage

IPknot can take FASTA formatted RNA sequences as input, the predict their secondary structures including pseudoknots.

% ipknot: [options] fasta
 -h:       show this message
 -t th:    threshold of base-pairing probabilities for each level
 -g gamma: weight for true base-pairs equivalent to -t 1/(gamma+1)
           (default: -g 4 -g 8)
 -m:       use McCaskill model (default: CONTRAfold model)
 -i:       allow isolated base-pairs
 -b:       output the prediction via BPSEQ format

% ipknot ASE00001.fa
> ASE_00001
gaggaaagucccgccUCCAGAUCAAGGGAAGUCCCGCGAGGGACAAGGGUAGUACCCUUGGCAACUGCACAGAAAACUUACCCCUAAAUAUUCAAUGAGGAUUUGAUUCGACUCUUACCUUGGCGACAAGGUAAGAUAGAUGAAGAGAAUAUUUAGGGGUUGAAACGCAGUCCUUCCCGGAGCAAGUAGGGGGGUCAAUGAGAAUGAUCUGAAGACCUCCCUUGACGCAUAGUCGAAUCCCCCAAAUacagaagcgggcuua
.....(((.(((((.((........[[(([[[[[[..((]]]](((((((...)))))))...(((((...........((((((((((((((..............((...((((((((((....))))))))))..))......))))))))))))))......))))).]]))]]...[[....(((((((((....(((....)))...))))))))).(((]]...)))...))...........)).)))))))).

References

• Sato, K., Kato, Y., Hamada, M., Akutsu, T., Asai, K.: IPknot: fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming, Bioinformatics, 27(13):i85-i93 (Jul. 2011)