RNALALIFOLD(1)

NAME
RNALalifold - manual page for RNALalifold 2.3.0

SYNOPSIS
RNALalifold [options] <file1.aln>

DESCRIPTION
RNALalifold 2.3.0

calculate locally stable secondary structures for a set of aligned RNAs

reads aligned RNA sequences from stdin or file.aln and calculates locally stable RNA secondary structure with a maximal base pair span. For a sequence of length n and a base pair span of L the algorithm uses only O(n+L*L) memory and O(n*L*L) CPU time. Thus it is practical to "scan" very large genomes for short RNA

    structures.

-h, --help
    Print help and exit

--detailed-help
    Print help, including all details and hidden options, and exit

--full-help
    Print help, including hidden options, and exit

-V, --version
    Print version and exit

  General Options:

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

-L, --span=INT
    Set the maximum allowed separation of a base pair to span. I.e. no pairs (i,j) with j-i>span will be allowed.

    (default=`70')

--csv
    Create comma separated output (csv)

    (default=off)

  Algorithms:

    Select additional algorithms which should be included in the calculations. The Minimum free energy (MFE) and a structure representative are calculated in any case.

--mis
    Output "most informative sequence" instead of simple consensus: For each column of the alignment output the set of nucleotides with frequence greater than average in IUPAC notation.

    (default=off)

  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, this is unsupported for the partition function folding.

    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 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 by default (as well as with -d1 and -d3) pf and mfe folding treat dangling ends differently. Use -d2 in addition to -p to ensure that both algorithms use the same energy model.

--noLP
    Produce structures without lonely pairs (helices of length 1).

    (default=off)

    For partition function folding this only disallows pairs that can only occur isolated. Other pairs may still occasionally occur as helices of length 1.

--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.

    A sample parameter file should accompany your distribution. See the RNAlib documentation for details on the file format.

--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.

--cfactor=DOUBLE
    Set the weight of the covariance term in the energy function

    (default=`1.0')

--nfactor=DOUBLE
    Set the penalty for non-compatible sequences in the covariance term of the energy function

    (default=`1.0')

-R, --ribosum_file=ribosumfile
    use specified Ribosum Matrix instead of normal

energy model. Matrixes to use should be 6x6
    matrices, the order of the terms is AU, CG, GC, GU, UA, UG.

-r, --ribosum_scoring
    use ribosum scoring matrix. The matrix is chosen according to the minimal and maximal pairwise identities of the sequences in the file.

    (default=off)

REFERENCES
If you use this program in your work you might want to cite: R. Lorenz, S.H. Bernhart, C. Hoener zu Siederdissen, H. Tafer, C. Flamm, P.F. Stadler and I.L. Hofacker (2011), "ViennaRNA Package 2.0", Algorithms for Molecular Biology: 6:26 I.L. Hofacker, W. Fontana, P.F. Stadler, S. Bonhoeffer, M. Tacker, P. Schuster (1994), "Fast Folding and Comparison of RNA Secondary Structures", Monatshefte f. Chemie: 125, pp 167-188 The energy parameters are taken from: D.H. Mathews, M.D. Disney, D. Matthew, J.L. Childs, S.J. Schroeder, J. Susan, M. Zuker, D.H. Turner (2004), "Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure", Proc. Natl. Acad. Sci. USA: 101, pp 7287-7292 D.H Turner, D.H. Mathews (2009), "NNDB: The nearest neighbor parameter database for predicting stability of nucleic acid secondary structure", Nucleic Acids Research: 38, pp 280-282

AUTHOR
Ivo L Hofacker, Ronny Lorenz

REPORTING BUGS
If in doubt our program is right, nature is at fault. Comments should be sent to rna@tbi.univie.ac.at.