
                                 vrnaheat 



Function

   RNA melting

Description

   This is a port of the Vienna RNA package program RNAheat.

Algorithm

   See the original documentation for the Vienna RNA package
   http://www.tbi.univie.ac.at/~ivo/RNA/

Usage

   Here is a sample session with vrnaheat


% vrnaheat -mintemp 30 -maxtemp 120 -step 0.1 -smoothing 4 
RNA melting
Input nucleotide sequence: cofold-red.fasta
Vienna RNAfold output file [red.vrnaheat]: 

   Go to the input files for this example
   Go to the output files for this example

Command line arguments

   Standard (Mandatory) qualifiers:
  [-sequence]          sequence   Nucleotide sequence filename and optional
                                  format, or reference (input USA)
  [-outfile]           outfile    [*.vrnaheat] Vienna RNAfold output file

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers:
   -paramfile          infile     Vienna RNA parameters file (optional)
   -mintemp            float      [0.0] Temperature (Any numeric value)
   -maxtemp            float      [100.0] Temperature (Any numeric value)
   -[no]gu             boolean    [Y] Allow GU pairs
   -[no]closegu        boolean    [Y] Allow GU pairs at end of helices
   -[no]lp             boolean    [Y] Allow lonely pairs
   -[no]convert        boolean    [Y] Convert T to U
   -nsbases            string     Non-standard bases (Any string is accepted)
   -[no]tetraloop      boolean    [Y] Stabilizing energies for tetra-loops
   -energy             menu       [0] Rarely used option to fold sequences
                                  from the ABCD... alphabet (Values: 0 (BP); 1
                                  (Any with GC); 2 (Any with AU parameters))
   -smoothing          integer    [2] Parabola fitting value (Any integer
                                  value)
   -step               float      [1.0] Step size in degrees C (Number from
                                  0.010 to 1000.000)
   -dangles            menu       [2] Method (Values: 0 (Ignore); 2 (Always
                                  use dangling energies))

   Associated qualifiers:

   "-sequence" associated qualifiers
   -sbegin1            integer    Start of the sequence to be used
   -send1              integer    End of the sequence to be used
   -sreverse1          boolean    Reverse (if DNA)
   -sask1              boolean    Ask for begin/end/reverse
   -snucleotide1       boolean    Sequence is nucleotide
   -sprotein1          boolean    Sequence is protein
   -slower1            boolean    Make lower case
   -supper1            boolean    Make upper case
   -sformat1           string     Input sequence format
   -sdbname1           string     Database name
   -sid1               string     Entryname
   -ufo1               string     UFO features
   -fformat1           string     Features format
   -fopenfile1         string     Features file name

   "-outfile" associated qualifiers
   -odirectory2        string     Output directory

   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write standard output
   -filter             boolean    Read standard input, write standard output
   -options            boolean    Prompt for standard and additional values
   -debug              boolean    Write debug output to program.dbg
   -verbose            boolean    Report some/full command line options
   -help               boolean    Report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning            boolean    Report warnings
   -error              boolean    Report errors
   -fatal              boolean    Report fatal errors
   -die                boolean    Report dying program messages

Input file format

   vrnaheat reads any normal sequence USAs.

  Input files for usage example

  File: cofold-red.fasta

>red
AUGAAGAUGA

Output file format

   vrnaheat outputs a graph to the specified graphics device. outputs a
   report format file. The default format is ...

  Output files for usage example

  File: red.vrnaheat

30.0    0.0249224
30.1    0.0246136
30.2    0.0243089
30.3    0.0240069
30.4    0.0237101
30.5    0.0234163
30.6    0.0231268
30.7    0.0228404
30.8    0.0225589
30.9    0.0222815
31.0    0.0220065
31.1    0.021735
31.2    0.0214681
31.3    0.0212039
31.4    0.0209434
31.5    0.0206865
31.6    0.0204337
31.7    0.0201827
31.8    0.0199348
31.9    0.0196913
32.0    0.0194505
32.1    0.0192131
32.2    0.0189785
32.3    0.0187473
32.4    0.0185188
32.5    0.0182933
32.6    0.0180709
32.7    0.0178514
32.8    0.0176344
32.9    0.0174205
33.0    0.0172092
33.1    0.0170016
33.2    0.0167953
33.3    0.0165932
33.4    0.0163923
33.5    0.0161944
33.6    0.0159986
33.7    0.0158057
33.8    0.0156164
33.9    0.0154291
34.0    0.0152431
34.1    0.0150599
34.2    0.0148787
34.3    0.0147011
34.4    0.0145247
34.5    0.0143517
34.6    0.014181
34.7    0.0140118
34.8    0.0138441
34.9    0.0136778


  [Part of this file has been deleted for brevity]

114.9   2.13689e-05
115.0   2.12864e-05
115.1   2.11928e-05
115.2   2.1109e-05
115.3   2.10593e-05
115.4   2.09632e-05
115.5   2.08829e-05
115.6   2.07866e-05
115.7   2.07026e-05
115.8   2.06099e-05
115.9   2.04914e-05
116.0   2.04207e-05
116.1   2.03585e-05
116.2   2.0273e-05
116.3   2.01923e-05
116.4   2.013e-05
116.5   2.00431e-05
116.6   1.99869e-05
116.7   1.98766e-05
116.8   1.98387e-05
116.9   1.97431e-05
117.0   1.96486e-05
117.1   1.95307e-05
117.2   1.94705e-05
117.3   1.93833e-05
117.4   1.93354e-05
117.5   1.92382e-05
117.6   1.92e-05
117.7   1.91249e-05
117.8   1.90645e-05
117.9   1.8945e-05
118.0   1.88858e-05
118.1   1.87982e-05
118.2   1.87032e-05
118.3   1.86216e-05
118.4   1.85672e-05
118.5   1.85041e-05
118.6   1.84348e-05
118.7   1.83235e-05
118.8   1.82862e-05
118.9   1.81883e-05
119.0   1.81275e-05
119.1   1.80642e-05
119.2   1.79773e-05
119.3   1.79189e-05
119.4   1.78418e-05
119.5   1.77561e-05
119.6   1.7721e-05
119.7   1.76402e-05
119.8   1.75803e-05
119.9   1.74981e-05

Data files

   For details of Vienna RNA file formats, see the original documentation
   http://www.tbi.univie.ac.at/~ivo/RNA/

Notes

   None.

References

   None.

Warnings

   None.

Diagnostic Error Messages

   None.

Exit status

   It always exits with status 0.

Known bugs

   None.

See also

    Program name                       Description
   einverted      Finds DNA inverted repeats
   vrnaalifold    RNA alignment folding
   vrnaalifoldpf  RNA alignment folding with partition
   vrnacofold     RNA cofolding
   vrnacofoldconc RNA cofolding with concentrations
   vrnacofoldpf   RNA cofolding with partitioning
   vrnadistance   RNA distances
   vrnaduplex     RNA duplex calculation
   vrnaeval       RNA eval
   vrnaevalpair   RNA eval with cofold
   vrnafold       Calculate secondary structures of RNAs
   vrnafoldpf     Secondary structures of RNAs with partition
   vrnainverse    RNA sequences matching a structure
   vrnalfold      Calculate locally stable secondary structures of RNAs
   vrnaplot       Plot vrnafold output
   vrnasubopt     Calculate RNA suboptimals

Author(s)

   This program is an EMBOSS conversion of a program written by Ivo
   Hofacker as part of his VIENNA package.

   Although we take every care to ensure that the results of the EMBOSS
   version are identical to those from the original package, we recommend
   that you check your inputs give the same results in both versions
   before publication.

   Please report all bugs in the EMBOSS version to the EMBOSS bug team,
   not to the original author.

History

   Converted (October 2005) by Alan Bleasby

Target users

   This program is intended to be used by everyone and everything, from
   naive users to embedded scripts.

Comments
