Content-type: text/html Manpage of RNAUP

RNAUP

Section: ViennaRNA (l)
Updated: 1.6
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NAME

RNAup - calculates the thermodynamics of RNA-RNA interactions

SYNOPSIS

RNAup [-u length] [-c "SHIME"] [-w length] [-b] [-5 length] [-3 length] [-X[p|f]] [-C] [-T temp] [-4] [-d[2|3]] [-noGU] [-noCloseGU] [-noLP] [-P paramfile] [-nsp pairs] [-S scale] [-ncov]

DESCRIPTION

RNAup calculates the thermodynamics of RNA-RNA interactions. RNA-RNA binding is decomposed into two stages. (1) First the probability that a sequence interval (e.g. a binding site) remains unpaired is computed. (2) Then the binding energy given that the binding site is unpaired is calculated as the optimum over all possible types of bindings.

RNAup provides two different modes: By default only the probability of being unpaired and the free energy to open a region of length -u are plotted to a file. The region of minimal free energy of unfolding is written to stdout.

In interaction mode interaction between two RNAs is calculated. It is invoked if two sequences seperated by "&" are given. By default the longer RNA is considered a structured target sequence, the shorter one an unstructured small RNA. The structure of the small RNA can be included using the -b option.
In this mode additionally the conditional probability of an interaction and the optimal free energy of binding at a given position are plotted to a file. Output to stdout consists of the optimal structure upon hybridization (using RNAduplex), the location and the free energy, dG, for the region of minimal free energy of interaction. (where dG = dGint + dGu_l; dGint: free energy of interaction, dGu_l: free energy necessary to open the longer sequence).

(Notice: The output to stdout is dG[i,j;k,l], where position i<j are in the longer sequence and positions k<l are in the shorter sequence. dG[i,j;k,l] is the largest contribution to dG[i,j] = sum_kl dG[i,j;k,l] which is given in the output file: therefore dG[i,j;k,l] <= dG[i,j].)

Each sequence should be in 5' to 3' direction. If the sequence is preceded by a line of the form
> name
the output file "name_up.out" is produced. Otherwise the file name defaults to RNA_up.out. Existing files of the same name will be overwritten.

RNA sequences are read from stdin as strings of characters, white space and newline within a sequence cause an error. Newline is used to separate sequences. The program will continue to read new sequences until a line consisting of the single character @ or an end of file condition is encountered.

OPTIONS

Options for probability of an unpaired region:

-u len: specifies the length (len) of the unstructured region in the output. The default value is 4. The probability of being unpaired is plotted on the right border of the unpaired region. You can specify up to 20 different length values: use "-" to specify a range of continuous values (e.g. -u 4-8) or specify a list of comma separated values (e.g. -u 4,8,15).
-c SHIME: by default only the full probability of being unpaired is plotted. The -c option allows to get the different contributions (c) to the probability of being unpaired: The full probability of being unpaired ("S") is the sum of the probability of being unpaired in the exterior loop ("E"), within a hairpin loop ("H"), within an interior loop ("I") and within a multiloop ("M"). Any combination of these letters may be given.
Options for calculation of interaction:
-w len: determines the maximal length of the region of interaction, the default is 25.
-b: include the probability of unpaired regions in both (b) RNAs. By default only the probability of being unpaired in the longer RNA (target) is used.
-5(-3) len: These options extend the region of interaction in the target by len residues to the 5' and 3' side, respectively. The underlying assumption is that it is favorable for an interaction if not only the direct region of contact is unpaired but also a few residues 5'and 3' of this region.
-Xp: set interaction mode. Pairwise (p) interaction is calculated: The first sequence interacts with the 2nd, the third with the 4th etc. If -Xp is selected two interacting sequences may be given in a single line separated by "&" or each sequence may be given on an extra line.
-Xf: set interaction mode. The interaction of each sequence with the first one is calculated (e.g. interaction of one mRNA with many small RNAs). Each sequence has to be given on an extra line.
general options:
-C: Calculate structures subject to constraints. Symbols ".", "x" and the matching brackets "( )" work in boths modes as described in RNAfold. Symbols "<" and ">" are soley used for the calculation of unpaired regions. The "|" constrain works only in interaction mode, the corresponding base has to be paired intermolecularily.

the -noGU, -noCloseGU, -nsp, -S, -P, -noLP, -T, -4, and -d options work as in RNAfold, see there for description.

REFERENCES

The energy parameters are taken from:
D.H. Mathews, J. Sabina, M. Zuker and H. Turner "Expanded Sequence Dependence of Thermodynamic Parameters Provides Robust Prediction of RNA Secondary Structure" JMB, 288, pp 911-940, 1999

If you use this program in your work you might want to cite:

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: 167-188

U.Mueckstein, H. Tafer, J. Hackermueller, S.H. Bernhart, P.F. Stadler, and I.L. Hofacker (2006) Thermodynamics of RNA-RNA Binding. Bioinformatics. doi:10.1093/bioinformatics/btl024

VERSION

This man page documents version @VERSION@ Vienna RNA Package.

AUTHORS

Ivo L Hofacker, Peter F Stadler, Ulrike Mueckstein.

BUGS

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

This document was created by man2html, using the manual pages.
Time: 09:45:42 GMT, December 13, 2007