EMBASSY: VIENNA: vrnaheat

vrnaheat

Wiki

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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

RNA melting
Version: EMBOSS:6.2.0

   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    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.

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.

Wiki

Function

Description

Algorithm

Usage

Command line arguments

Input file format

Input files for usage example

File: cofold-red.fasta

Output file format

Output files for usage example

File: red.vrnaheat

Data files

Notes

References

Warnings

Diagnostic Error Messages

Exit status

Known bugs

See also

Author(s)

History

Target users

Comments