                                  ovrnaheat



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Function

   Calculate specific heat of RNA melting

Description

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

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

Algorithm

   The program will continue to read new sequences until a line consisting
   of the single character "@" or an end of file condition is encountered.

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

Usage

   Here is a sample session with ovrnaheat


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


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

Command line arguments

Calculate specific heat of RNA melting
Version: EMBOSS:6.6.0.0

   Standard (Mandatory) qualifiers:
  [-sequence]          sequence   Nucleotide sequence filename and optional
                                  format, or reference (input USA)
  [-outfile]           outfile    [*.ovrnaheat] 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)
   -[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
   -scircular1         boolean    Sequence is circular
   -squick1            boolean    Read id and sequence only
   -sformat1           string     Input sequence format
   -iquery1            string     Input query fields or ID list
   -ioffset1           integer    Input start position offset
   -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 and exit. 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
   -version            boolean    Report version number and exit


Input file format

   ovrnaheat reads any normal sequence USAs.

  Input files for usage example

  File: cofold-red.fasta

>red
AUGAAGAUGA

Output file format

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

  Output files for usage example

  File: red.ovrnaheat

30.0    0.0249226
30.1    0.0246153
30.2    0.0243077
30.3    0.0240077
30.4    0.0237102
30.5    0.0234176
30.6    0.0231288
30.7    0.022845
30.8    0.0225598
30.9    0.0222795
31.0    0.0220043
31.1    0.0217381
31.2    0.0214691
31.3    0.0212051
31.4    0.0209456
31.5    0.0206852
31.6    0.0204331
31.7    0.0201802
31.8    0.0199351
31.9    0.0196904
32.0    0.0194501
32.1    0.0192143
32.2    0.0189796
32.3    0.0187481
32.4    0.0185177
32.5    0.0182931
32.6    0.0180723
32.7    0.0178506
32.8    0.0176348
32.9    0.0174194
33.0    0.0172098
33.1    0.0170001
33.2    0.0167962
33.3    0.0165928
33.4    0.0163919
33.5    0.0161935
33.6    0.0159983
33.7    0.0158062
33.8    0.015616
33.9    0.0154289
34.0    0.0152444
34.1    0.0150598
34.2    0.014879
34.3    0.0147013
34.4    0.0145256
34.5    0.0143517
34.6    0.0141817
34.7    0.0140109
34.8    0.0138439
34.9    0.0136775


  [Part of this file has been deleted for brevity]

114.9   2.13815e-05
115.0   2.12305e-05
115.1   2.1236e-05
115.2   2.10849e-05
115.3   2.09859e-05
115.4   2.09391e-05
115.5   2.08923e-05
115.6   2.07932e-05
115.7   2.07462e-05
115.8   2.05948e-05
115.9   2.04955e-05
116.0   2.03962e-05
116.1   2.03491e-05
116.2   2.01973e-05
116.3   2.01502e-05
116.4   2.01554e-05
116.5   2.01605e-05
116.6   2.00086e-05
116.7   1.99613e-05
116.8   1.98092e-05
116.9   1.97619e-05
117.0   1.96621e-05
117.1   1.96147e-05
117.2   1.95148e-05
117.3   1.93624e-05
117.4   1.93148e-05
117.5   1.93198e-05
117.6   1.92197e-05
117.7   1.90671e-05
117.8   1.91245e-05
117.9   1.89717e-05
118.0   1.88189e-05
118.1   1.87711e-05
118.2   1.87233e-05
118.3   1.86755e-05
118.4   1.8575e-05
118.5   1.84745e-05
118.6   1.84265e-05
118.7   1.83786e-05
118.8   1.82779e-05
118.9   1.81772e-05
119.0   1.81819e-05
119.1   1.80811e-05
119.2   1.79275e-05
119.3   1.79848e-05
119.4   1.78311e-05
119.5   1.78357e-05
119.6   1.76819e-05
119.7   1.76336e-05
119.8   1.75324e-05
119.9   1.74313e-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
   banana           Plot bending and curvature data for B-DNA
   btwisted         Calculate the twisting in a B-DNA sequence
   einverted        Find inverted repeats in nucleotide sequences
   ovrnaalifold     Calculate secondary structures for a set of aligned RNAs
   ovrnaalifoldpf   Calculate secondary structures for a set of aligned RNAs
                    (partition)
   ovrnacofold      Calculate secondary structures of RNA dimers
   ovrnacofoldconc  Calculate secondary structures of RNA dimers
                    (concentrations)
   ovrnacofoldpf    Calculate secondary structures of RNA dimers
                    (partitioning)
   ovrnadistance    Calculate distances between RNA secondary structures
   ovrnaduplex      Predict RNA duplex (hybridization) sites and structure
   ovrnaeval        Calculate energy of RNA sequences with a given secondary
                    structure
   ovrnaevalpair    Calculate energy of RNA sequences on given secondary
                    structure
   ovrnafold        Calculate min. energy RNA structure / pair probabilities
                    (partition)
   ovrnafoldpf      Calculate min. energy RNA structure / pair probabilities
   ovrnainverse     Find RNA sequences with a given secondary structure
   ovrnalfold       Calculate locally stable secondary structures of RNAs
   ovrnaplot        Draw RNA secondary structures
   ovrnasubopt      Calculate suboptimal secondary structure of RNA
   sirna            Find siRNA duplexes in mRNA
   vrna2dfold       Calculate RNA structures and samples of k,l neighbourhoods
   vrnaaliduplex    RNA duplex calculation for two sequence alignments
   vrnaalifold      Calculate secondary structures for a set of aligned RNAs
   vrnaalifoldpf    Calculate secondary structures for a set of aligned RNAs
                    (partition)
   vrnacofold       Calculate secondary structures of RNA dimers
   vrnacofoldconc   Calculate secondary structures of RNA dimers
                    (concentrations)
   vrnacofoldpf     Calculate secondary structures of RNA dimers
                    (partitioning)
   vrnadistance     Calculate distances between RNA secondary structures
   vrnaduplex       Predict RNA duplex (hybridization) sites and structure
   vrnaeval         Calculate energy of RNA sequences with a given secondary
                    structure
   vrnaevalpair     Calculate energy of RNA sequences on given secondary
                    structure
   vrnafold         Calculate min. energy RNA secondary structures and pair
                    probabilities
   vrnafoldpf       Calculate min. energy RNA structures / pair probabilities
                    (partition)
   vrnaheat         Calculate specific heat of RNA melting
   vrnainverse      Find RNA sequences with a given secondary structure
   vrnalalifoldpf   Calculate secondary structures for a set of aligned RNAs
                    (partition)
   vrnalfold        Calculate locally stable secondary structures of RNAs
   vrnalfoldz       Calculate locally stable secondary structures of RNAs plus
                    zscore
   vrnapkplex       Calculate RNA structures plus pseudoknots
   vrnaplfold       Compute avg. pair probabilities for local base pairs in RNA
                    sequences
   vrnaplot         Draw RNA secondary structures
   vrnasubopt       Calculate suboptimal secondary structures of RNAs

Author(s)

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

   Please report all bugs to the EMBOSS bug team
   (emboss-bug (c) emboss.open-bio.org) 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
