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RNAheat - calculate specific heat of RNAs
RNAheat [-Tmin t1] [-Tmax t2] [-h
stepsize] [-m ipoints] [-d] [-4] [-noGU] [-noCloseGU]
[-nsp pairs] [-P paramfile] [-e 1|2]
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
- -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.
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.
The partition function algorithm is based on work by J.S.
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,
This man page documents version 1.8.5 Vienna RNA Package.
Ivo L Hofacker, Peter F Stadler.
If in doubt our program is right, nature is at fault. Comments
should be sent to email@example.com.
This document was created by man2html,
using the manual pages.
Time: 07:19:16 GMT, February 23, 2011