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 first file to standard output
   -filter             boolean    Read first file from standard input, write
                                  first file to 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

Standard (Mandatory) qualifiers Allowed values Default
[-sequence]
(Parameter 1)		 Nucleotide sequence filename and optional format, or reference (input USA) Readable sequence Required
[-outfile]
(Parameter 2)		 Vienna RNAfold output file Output file <*>.vrnaheat
Additional (Optional) qualifiers Allowed values Default
(none)
Advanced (Unprompted) qualifiers Allowed values Default
-paramfile Vienna RNA parameters file (optional) Input file Required
-mintemp Temperature Any numeric value 0.0
-maxtemp Temperature Any numeric value 100.0
-[no]gu Allow GU pairs Boolean value Yes/No Yes
-[no]closegu Allow GU pairs at end of helices Boolean value Yes/No Yes
-[no]lp Allow lonely pairs Boolean value Yes/No Yes
-[no]convert Convert T to U Boolean value Yes/No Yes
-nsbases Non-standard bases Any string is accepted An empty string is accepted
-[no]tetraloop Stabilizing energies for tetra-loops Boolean value Yes/No Yes
-energy Rarely used option to fold sequences from the ABCD... alphabet
0 (BP)
1 (Any with GC)
2 (Any with AU parameters)
 0
-smoothing Parabola fitting value Any integer value 2
-step Step size in degrees C Number from 0.010 to 1000.000 1.0
-dangles Method
0 (Ignore)
2 (Always use dangling energies)
 2

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 inverted repeats in nucleotide sequences
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