RNA-RNA interaction prediction by integer programming
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README.md

RactIP for predicting RNA-RNA interaction using integer programming

Requirements

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

Then,

make
make install

Usage

RactIP can take two FASTA formatted RNA sequences as input, the predict their joint secondary structures.

Usage: ractip [OPTIONS]... [FILES]...

-h, --help                 Print help and exit
    --full-help            Print help, including hidden options, and exit
-V, --version              Print version and exit
-a, --alpha=FLOAT          weight for hybridization  (default=`0.6')
-b, --beta=FLOAT           weight for accessibility  (default=`0.0')
-t, --fold-th=FLOAT        Threshold for base-pairing probabilities
                           (default=`0.8')
-u, --hybridize-th=FLOAT   Threshold for hybridazation probabilities
                           (default=`0.3')
-s, --acc-th=FLOAT         Threshold for accessible probabilities
                           (default=`0.005')
-e, --show-energy          calculate the free energy of the predicted joint
                           structure  (default=off)

% ractip DIS.fa DIS.fa
>DIS
CUCGGCUUGCUGAGGUGCACACAGCAAGAGGCGAG
((((.(((((((..[[[[[[.)))))))...))))
>DIS
CUCGGCUUGCUGAGGUGCACACAGCAAGAGGCGAG
((((.(((((((..]]]]]].)))))))...))))

The parenthesis '()' and the brackets '[]' indicate the predicted internal base-pairs and external base-pairs (interactions), respectively.

References

  • Kato, Y., Sato, K., Hamada, M., Watanabe, Y., Asai, K., Akutsu, T.: RactIP: fast and accurate prediction of RNA-RNA interaction using integer programming. Bioinformatics, 26(18):i460-i466, 2010.