RNAHEAT

Vienna RNA (l) Return to Main Contents

NAME

RNAheat - calculate specific heat of RNAs

SYNOPSIS

RNAheat [-Tmin t1] [-Tmax t2] [-h stepsize] [-m ipoints] [-d] [-4] [-noGU] [-noCloseGU] [-nsp pairs] [-P paramfile] [-e 1|2]

DESCRIPTION

RNAheat reads RNA sequences from stdin and calculates their specific heat in the temperature range t1 to t2, from the partition function by numeric differentiation. The result is written to stdout as a list of pairs of temperature in C and specific heat in Kcal/(Mol*K).
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

-Tmin t1
Lowest temperature, default is 0C.
-Tmax t2
Highest temperature, default is 100C.
-h stepsize
Calculate partition function every stepsize degrees C. Default is 1C.
-m ipoints
The program fits a parabola to 2*ipoints+1 data points to calculate 2nd derivatives. Increasing this parameter produces a smoother curve. Default is 2.

The -d, -4, -noGU, -noCloseGU, -e, -P, -nsp, options work as in RNAfold.

EXAMPLES

   RNAheat -Tmin -30 -Tmax 120 -h 0.1 -m 4 < tRNA.seq | xmgrace -pipe
produces plots of the specific heat of the sequences in tRNA.seq.

REFERENCES

The partition function algorithm is based on work by J.S. McCaskill.

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

J.S. McCaskill (1990) The equilibrium partition function and base pair binding probabilities for RNA secondary structures, Biopolymers 29: 1105-1119
D. Adams (1979) The hitchhiker's guide to the galaxy, Pan Books, London

VERSION

This man page documents version 1.8.5 Vienna RNA Package.

AUTHORS

Ivo L Hofacker, Peter F Stadler.

SEE ALSO

RNAfold(l),

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: 07:19:16 GMT, February 23, 2011