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')s&+` 21D wD* 3 $3 , )s~$, QbHHI I JJ K~L Mb MbNb Nb( O~0OP~-R@%valS~.Tb.U/{ {0xM*b~D$ %ib1w2t'ib34ib34ib5-b+b++~,$, * 5bb~$.b6d  5bb~$7d< 'retb.b8(7d< 5bb$7d< 9.-.-9.s.b5Tbb~$b7d< .'p$. $. b. b. b. b5{bybyy~zb7dz< 'c|.}~,bbD3 ~%cb.b- |-b|.b.b-b|$$b$b$b:&l$b ;/.qeYMA(<};#(<</ (=< =<#=/<;<<T~?rf(=<@.?-.?-@.E-.E-@A.L-.L->.Z-.Z-@.h-.h-@.v-.v-@.-.-@$.-.-@R.-.-@.-.->.s.b-4 *gbbDbbb$b-KP!bwbD*4bbD3 $b D -K -\b -bb -hb -3 AAAB~ B~  ~ Bu  ;~ BY+  a~ B!Q B~  /usr/include/usr/include/bits/usr/lib/gcc/x86_64-redhat-linux/4.1.2/includeRNAheat_cmdl.cstdlib.hRNAheat_cmdl.hstdio.hlibio.htypes.hstddef.h fXvqtvvtZUuwruvtvvu tytouuu tvtvuuuuwxt tq thtu tutuuvuuuuux uYxuuuxtv_vuuutu tuuvquvKYF=ZHN JKvtKKuzouuuu>tZguuuZ:YL9;? <rXX=:L=9e<J>VLWK:Lf Js=:L>8}Y"o]E3y<rrVVrrrrVV)O' =Yv >="Ʉ:>5/oW? (vt <v< +Y=c< kYK84#;`y#בYpg'1yjzCX@:>4;/[xJ~+KZuIS"YWrf"YWrf"YWf<p<Xk<vn.Xqy~\~tvsh~t_f~f^fvz.} g}dmsJ Js>Ys>eg/kQsue`ztl-t:Ivegf\}{<(#&J${D.$|G)$G XCSYxYtxO=]bYZ_a\":>Z_) %s="%s" %s RNAheathelpdetailed-helpfull-helpversionTminTmaxstepsizeipointsnoconvnoTetradanglesnoLPnoGUnoClosingGUparamFilenspenergyModelw2.0.0%s %s %s %s --%s: option `%s' is ambiguous hVm:4d:P:e:%s: invalid option -- %c 201001.%s: option unknown: %c%s Usage: RNAheat [options] General Options: Model Details:%s: cannot dump options to stream %s: `--%s' (`-%c') option given more than once%s %s: `--%s' option given more than once%s %s: invalid numeric value: %s %s: cannot open file for writing: %s %s: option `--%s' doesn't allow an argument %s: option `%c%s' doesn't allow an argument %s: option `%s' requires an argument %s: unrecognized option `--%s' %s: option requires an argument -- %c calculate specific heat of RNAsReads 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. -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 Below are command line options which alter the general behavior of this program --Tmin=t1 Lowest temperature (default=`0') --Tmax=t2 Highest temperature (default=`100') --stepsize=FLOAT Calculate partition function every stepsize degrees C (default=`1.') -m, --ipoints=ipoints The program fits a parabola to 2*ipoints+1 data points to calculate 2nd derivatives. Increasing this parameter produces a smoother curve (default=`2') --noconv Do not automatically substitude nucleotide "T" with "U" (default=off) -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 -d2 dangling energies will be added for the bases adjacent to a helix on both sides in any case -d0 ignores dangling ends altogether (mostly for debugging). --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. References: The partition function algorithm is based on work by J.S. McCaskill. J.S. McCaskill, (1990), "The equilibrium partition function and base pair binding probabilities for RNA secondary structures", Biopolymers 29: 1105-1119 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 D. Adams, (1979), "The hitchhiker's guide to the galaxy", Pan Books, London See also: RNAfold(1) Written by: Ivo L Hofacker, Peter F Stadler. Report bugs: If in doubt our program is right, nature is at fault. 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