General Options:

Below are command line options which alter the general behavior of this program

-R, --repeat[=INT]

Search repeatedly for the same structure. If an argument is supplied to this option it must follow the option flag immediately. E.g.: -R5

(default=`100')

If repeats is negative search until --repeats exact solutions are found, no output is done for unsuccessful searches. Be aware, that the program will not terminate if the target structure can not be found. If no value is supplied with this option, the default value is used.

-a, --alphabet=ALPHABET

Find sequences using only nucleotides from a given alphabet.

-v, --verbose

In conjunction with a negative value supplied to -R, print the last subsequence and substructure for each unsuccessful search.

(default=off)

Algorithms:

Select additional algorithms which should be included in the calculations.

-F, --function=mp

Use minimum energy (-Fm), partition function folding (-Fp) or both (-Fmp).

(default=`m')

In partition function mode, the probability of the target structure exp(-E(S)/kT)/Q is maximized. This probability is written in brackets after the found sequence and Hamming distance. In most cases you'll want to use the -f option in conjunction with -Fp, see below.

-f, --final=FLOAT

In combination with -Fp stop search when sequence is found with E(s)-F is smaller than final, where F=-kT*ln(Q).

Model Details:

-T, --temp=DOUBLE

Rescale energy parameters to a temperature of temp C. Default is 37C.

-4, --noTetra

Do not include special tabulated stabilizing energies for tri-, tetra- and hexaloop hairpins. Mostly for testing.

(default=off)

-d, --dangles=INT

How to treat "dangling end" energies for bases adjacent to helices in free ends and multi-loops

(default=`2')

With -d1 only unpaired bases can participate in at most one dangling end. With -d2 this check is ignored, dangling energies will be added for the bases adjacent to a helix on both sides in any case; this is the default for mfe and partition function folding (-p). The option -d0 ignores dangling ends altogether (mostly for debugging). With -d3 mfe folding will allow coaxial stacking of adjacent helices in multi-loops. At the moment the implementation will not allow coaxial stacking of the two interior pairs in a loop of degree 3 and works only for mfe folding.

Note that with -d1 and -d3 only the MFE computations will be using this setting while partition function uses -d2 setting, i.e. dangling ends will be treated differently.

--noGU

Do not allow GU pairs

(default=off)

--noClosingGU

Do not allow GU pairs at the end of helices

(default=off)

-P, --paramFile=paramfile

Read energy parameters from paramfile, instead of using the default parameter set.

Different sets of energy parameters for RNA and DNA should accompany your distribution. See the RNAlib documentation for details on the file format. When passing the placeholder file name "DNA", DNA parameters are loaded without the need to actually specify any input file.

--nsp=STRING

Allow other pairs in addition to the usual AU,GC,and GU pairs.

Its argument is a comma separated list of additionally allowed pairs. If the first character is a "-" then AB will imply that AB and BA are allowed pairs. e.g. RNAfold -nsp -GA will allow GA and AG pairs. Nonstandard pairs are given 0 stacking energy.

-e, --energyModel=INT

Rarely used option to fold sequences from the artificial ABCD... alphabet, where A pairs B, C-D etc. Use the energy parameters for GC (-e 1) or AU (-e 2) pairs.