Fold
A folding simulation program for the prediction of RNA secondary structures
and the reconstruction of RNA tertiary structures.
OPTIONS
- -i file
-
Read the sequence of bases (and optionally the sequence of turn directions)
in seq or seq2 format from file.
- -i2 file
-
Read base pairs in bp format from file for reconstruction.
- -o file
-
Write lattice conformation
(a sequence of bases and a sequence of turn directions)
in seq2 format to file.
- -o2 file
-
Write base pairs (realized by lattice conformation)
in bp format to file.
- -movie
-
Turn on movie mode.
Write the movie sequence of pull moves to stdout;
each line of the output
contains two numbers for the base index and the turn direction
of a pull move.
By default, movie is off.
- -v
-
Write verbose messages of folding simulation to stderr.
By default, verbose is off.
- -a repeats [steps]
-
Repeat the annealing procedure for multiple iterations
and use the given number of steps in each iteration.
By default, the number of repeats (iterations) is 5,
and the number of steps in each iteration is 100 times the square of
the sequence length.
- -d
-
Turn on doubling steps for folding simulation.
By default, doubling is off.
- -e
-
Turn on early-terminate for reconstruction so that
the annealing procedure is stopped
as soon as a good lattice conformation is reconstructed.
By default, early-terminate is off.
- -s seed
-
Initialize random number generator with seed instead of the current time.
- -2
-
Use 2D triangular lattice instead of 3D triangular lattice.
EXAMPLES
- ./fold.exe -i xxx.seq -o xxx.seq2 -o2 xxx.bp -d
-
Perform folding simulation (predict mode) on sequence xxx.seq,
use doubling steps,
write lattice conformation to xxx.seq2
and predicted base pairs to xxx.bp.
- ./fold.exe -i xxx.seq -i2 xxx.bp -o xxx.seq2 -e
-
Perform folding simulation (reconstruct mode) on sequence xxx.seq
with base pairs xxx.bp, use early-terminate,
write reconstructed lattice conformation to xxx.seq2.
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