vrnaheat

 

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Function

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 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

RNA melting
Version: EMBOSS:6.4.0.0

   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)
   -[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 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 <*>.vrnaheat
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
-sformat1
-sformat_sequence
string Input sequence format Any string  
-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

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   0.013999
30.1   0.0139019
30.2   0.0138126
30.3   0.013718
30.4   0.0136311
30.5   0.013539
30.6   0.0134494
30.7   0.0133571
30.8   0.0132726
30.9   0.0131854
31   0.0130982
31.1   0.0130109
31.2   0.0129236
31.3   0.0128388
31.4   0.0127566
31.5   0.0126743
31.6   0.0125867
31.7   0.0125096
31.8   0.0124245
31.9   0.012342
32   0.0122647
32.1   0.0121794
32.2   0.0120994
32.3   0.0120219
32.4   0.0119417
32.5   0.0118668
32.6   0.0117865
32.7   0.0117114
32.8   0.0116363
32.9   0.0115585
33   0.0114833
33.1   0.0114107
33.2   0.0113327
33.3   0.01126
33.4   0.0111859
33.5   0.0111104
33.6   0.0110375
33.7   0.0109712
33.8   0.0108969
33.9   0.0108291
34   0.0107573
34.1   0.0106869
34.2   0.0106163
34.3   0.010551
34.4   0.0104817
34.5   0.0104123
34.6   0.0103469
34.7   0.0102801
34.8   0.0102133
34.9   0.0101477


  [Part of this file has been deleted for brevity]

114.9   0.000651667
115   0.000656008
115.1   0.00066536
115.2   0.000672212
115.3   0.000678232
115.4   0.000682584
115.5   0.000687773
115.6   0.000693802
115.7   0.000699833
115.8   0.000705867
115.9   0.000711068
116   0.000715435
116.1   0.000722314
116.2   0.000723337
116.3   0.000729385
116.4   0.000734598
116.5   0.000738976
116.6   0.000741679
116.7   0.000748576
116.8   0.000752122
116.9   0.00075567
117   0.000757541
117.1   0.00076277
117.2   0.000765484
117.3   0.000768198
117.4   0.000770075
117.5   0.000773632
117.6   0.000778031
117.7   0.000779911
117.8   0.000782632
117.9   0.000785355
118   0.000787238
118.1   0.000788281
118.2   0.000789324
118.3   0.00079205
118.4   0.000794778
118.5   0.000795824
118.6   0.000796027
118.7   0.000797915
118.8   0.000799804
118.9   0.000802537
119   0.000802742
119.1   0.00080632
119.2   0.000809901
119.3   0.000812639
119.4   0.000816222
119.5   0.000819807
119.6   0.000821705
119.7   0.000827827
119.8   0.000828883
119.9   0.000832474

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
dan Calculates nucleic acid melting temperature
einverted Finds inverted repeats in nucleotide sequences
ovrnaalifold RNA alignment folding
ovrnaalifoldpf RNA alignment folding with partition
ovrnacofold RNA cofolding
ovrnacofoldconc RNA cofolding with concentrations
ovrnacofoldpf RNA cofolding with partitioning
ovrnadistance RNA distances
ovrnaduplex RNA duplex calculation
ovrnaeval RNA eval
ovrnaevalpair RNA eval with cofold
ovrnafold Calculate secondary structures of RNAs
ovrnafoldpf Secondary structures of RNAs with partition
ovrnaheat RNA melting
ovrnainverse RNA sequences matching a structure
ovrnalfold Calculate locally stable secondary structures of RNAs
ovrnaplot Plot vrnafold output
ovrnasubopt Calculate RNA suboptimals
sirna Finds siRNA duplexes in mRNA
vrna2dfold Structures and samples of k,l neighbourhoods
vrnaaliduplex RNA duplex calculation for two sequence alignments
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
vrnalalifoldpf Locally stable 2ry structures for a set of aligned RNAs
vrnalfold Calculate locally stable secondary structures of RNAs
vrnalfoldz Locally stable secondary structures of RNAs plus zscore
vrnapkplex RNA structures plus pseudoknots
vrnaplfold Locally stable RNA 2ry structures - pair probabilities
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.

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