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

Qualifier Type Description Allowed values Default
Standard (Mandatory) qualifiers
[-sequence]
(Parameter 1)
sequence Nucleotide sequence filename and optional format, or reference (input USA) Readable sequence Required
[-outfile]
(Parameter 2)
outfile Vienna RNAfold output file Output file <*>.ovrnaheat
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
-paramfile infile Vienna RNA parameters file (optional) Input file Required
-mintemp float Temperature Any numeric value 0.0
-maxtemp float Temperature Any numeric value 100.0
-[no]gu boolean Allow GU pairs Boolean value Yes/No Yes
-[no]closegu boolean Allow GU pairs at end of helices Boolean value Yes/No Yes
-[no]lp boolean Allow lonely pairs Boolean value Yes/No Yes
-[no]convert boolean Convert T to U Boolean value Yes/No Yes
-nsbases string Non-standard bases Any string  
-[no]tetraloop boolean Stabilizing energies for tetra-loops Boolean value Yes/No Yes
-energy list Rarely used option to fold sequences from the ABCD... alphabet
0 (BP)
1 (Any with GC)
2 (Any with AU parameters)
0
-smoothing integer Parabola fitting value Any integer value 2
-step float Step size in degrees C Number from 0.010 to 1000.000 1.0
-dangles list Method
0 (Ignore)
2 (Always use dangling energies)
2
Associated qualifiers
"-sequence" associated sequence qualifiers
-sbegin1
-sbegin_sequence
integer Start of the sequence to be used Any integer value 0
-send1
-send_sequence
integer End of the sequence to be used Any integer value 0
-sreverse1
-sreverse_sequence
boolean Reverse (if DNA) Boolean value Yes/No N
-sask1
-sask_sequence
boolean Ask for begin/end/reverse Boolean value Yes/No N
-snucleotide1
-snucleotide_sequence
boolean Sequence is nucleotide Boolean value Yes/No N
-sprotein1
-sprotein_sequence
boolean Sequence is protein Boolean value Yes/No N
-slower1
-slower_sequence
boolean Make lower case Boolean value Yes/No N
-supper1
-supper_sequence
boolean Make upper case Boolean value Yes/No N
-scircular1
-scircular_sequence
boolean Sequence is circular Boolean value Yes/No N
-squick1
-squick_sequence
boolean Read id and sequence only Boolean value Yes/No N
-sformat1
-sformat_sequence
string Input sequence format Any string  
-iquery1
-iquery_sequence
string Input query fields or ID list Any string  
-ioffset1
-ioffset_sequence
integer Input start position offset Any integer value 0
-sdbname1
-sdbname_sequence
string Database name Any string  
-sid1
-sid_sequence
string Entryname Any string  
-ufo1
-ufo_sequence
string UFO features Any string  
-fformat1
-fformat_sequence
string Features format Any string  
-fopenfile1
-fopenfile_sequence
string Features file name Any string  
"-outfile" associated outfile qualifiers
-odirectory2
-odirectory_outfile
string Output directory Any string  
General qualifiers
-auto boolean Turn off prompts Boolean value Yes/No N
-stdout boolean Write first file to standard output Boolean value Yes/No N
-filter boolean Read first file from standard input, write first file to standard output Boolean value Yes/No N
-options boolean Prompt for standard and additional values Boolean value Yes/No N
-debug boolean Write debug output to program.dbg Boolean value Yes/No N
-verbose boolean Report some/full command line options Boolean value Yes/No Y
-help boolean Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose Boolean value Yes/No N
-warning boolean Report warnings Boolean value Yes/No Y
-error boolean Report errors Boolean value Yes/No Y
-fatal boolean Report fatal errors Boolean value Yes/No Y
-die boolean Report dying program messages Boolean value Yes/No Y
-version boolean Report version number and exit Boolean value Yes/No N

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 © 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