sibRNAfold Files

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\f0\fs24 \cf0 The program "modified_nussinov.c" implements a modified version of the Nussinov algorithm that allows for conditional execution of the innermost loop and thus achieves a significant speed up. \
For more information on the Nussinov algorithm please refer to:\

\i Nussinov, R., et al. (1978) Algorithms for Loop Matchings, Siam J Appl Math, 35, 68-82.
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How to run:\
********************************\
To compile the modified nussinov program type the following:\
\
gcc modified_nussinov.c -o mnussinov\
\
To run the program:\
\
./mnussinov <input.seq\
\
\
Input and output:\
**********************************\
Input to the program is a file containing the RNA sequence to be folded.\
The program outputs the following:\
- the best folding score\
- the number of multiloop executions\
- information whether the folding resulted in a closed structure (1 or 0)\
- the folded structure\
\
For more information please contact:\
philipp.bucher@epfl.ch or slavica.dimitrieva@epfl.ch\
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