EMBASSY: VIENNA: ovrnacofoldconc

| ovrnacofoldconc

## Wiki

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## Function

Calculate secondary structures of RNA dimers (concentrations)

## Description

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

It reads two RNA sequences wich are then allowed to form a dimer structure, calculates their minimum free energy (mfe) dimer structure and output the mfe structure in bracket notation and its free energy. It produces plots of the resulting secondary structure graph and a "dot plot" of the base pairing matrix. Since dimer formation is concentration dependent, it can be used to compute equilibrium concentrations for all five monomer and (homo/hetero)-dimer species, given input concentrations for the monomers.

The original program has additional inputs and produces different outputs, depending on the options selected. In the EMBASSY implementation it is split into ovrnacofold ovrnacofoldconc and ovrnacofoldpf

## 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 ovrnacofoldconc

    % ovrnacofoldconc
    Calculate secondary structures of RNA dimers (concentrations)
    Input nucleotide sequence: cofold-red.fasta
    Second nucleotide sequence: cofold-blue.fasta
    Vienna RNA concentration data file: cofold-conc.dat
    Vienna RNAfold output file [red.ovrnacofoldconc]:

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

## Command line arguments

    Calculate secondary structures of RNA dimers (concentrations)
    Version: EMBOSS:6.6.0.0

       Standard (Mandatory) qualifiers:
      [-asequence]         sequence   Nucleotide sequence filename and optional
                                      format, or reference (input USA)
      [-bsequence]         sequence   Nucleotide sequence filename and optional
                                      format, or reference (input USA)
      [-concentrationfile] infile     Vienna RNA concentration data file
      [-outfile]           outfile    [*.ovrnacofoldconc] Vienna RNAfold output
                                      file

       Additional (Optional) qualifiers: (none)
       Advanced (Unprompted) qualifiers:
       -aconstraintfile    infile     Vienna RNA structure constraints file
                                      (optional)
       -bconstraintfile    infile     Second vienna RNA structure constraints file
                                      (optional)
       -paramfile          infile     Vienna RNA parameters file (optional)
       -temperature        float      [37.0] 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))
       -scale              float      [1.07] Estimate of ensemble free energy (Any
                                      numeric value)
       -dangles            menu       [1] Method (Values: 0 (Ignore); 1 (Only
                                      unpaired bases for just one dangling end); 2
                                      (Always use dangling energies); 3 (Allow
                                      coaxial stacking of adjacent helices))
       -ssoutfile          outfile    [*.ovrnacofoldconc] Vienna structure
                                      postscript output file
       -aoutfile           outfile    [*.ovrnacofoldconc] First (a) vienna dotplot
                                      output file
       -aaoutfile          outfile    [*.ovrnacofoldconc] Second (a-a) vienna
                                      dotplot output file
       -boutfile           outfile    [*.ovrnacofoldconc] Third (b) vienna dotplot
                                      output file
       -bboutfile          outfile    [*.ovrnacofoldconc] Fourth (b-b) vienna
                                      dotplot output file
       -aboutfile          outfile    [*.ovrnacofoldconc] Fifth (a-b) vienna
                                      dotplot output file

       Associated qualifiers:

       "-asequence" 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

       "-bsequence" associated qualifiers
       -sbegin2            integer    Start of the sequence to be used
       -send2              integer    End of the sequence to be used
       -sreverse2          boolean    Reverse (if DNA)
       -sask2              boolean    Ask for begin/end/reverse
       -snucleotide2       boolean    Sequence is nucleotide
       -sprotein2          boolean    Sequence is protein
       -slower2            boolean    Make lower case
       -supper2            boolean    Make upper case
       -scircular2         boolean    Sequence is circular
       -squick2            boolean    Read id and sequence only
       -sformat2           string     Input sequence format
       -iquery2            string     Input query fields or ID list
       -ioffset2           integer    Input start position offset
       -sdbname2           string     Database name
       -sid2               string     Entryname
       -ufo2               string     UFO features
       -fformat2           string     Features format
       -fopenfile2         string     Features file name

       "-outfile" associated qualifiers
       -odirectory4        string     Output directory

       "-ssoutfile" associated qualifiers
       -odirectory         string     Output directory

       "-aoutfile" associated qualifiers
       -odirectory         string     Output directory

       "-aaoutfile" associated qualifiers
       -odirectory         string     Output directory

       "-boutfile" associated qualifiers
       -odirectory         string     Output directory

       "-bboutfile" associated qualifiers
       -odirectory         string     Output directory

       "-aboutfile" associated qualifiers
       -odirectory         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
[-asequence] (Parameter 1) | sequence | Nucleotide sequence filename and optional format, or reference (input USA) | Readable sequence | Required
[-bsequence] (Parameter 2) | sequence | Nucleotide sequence filename and optional format, or reference (input USA) | Readable sequence | Required
[-concentrationfile] (Parameter 3) | infile | Vienna RNA concentration data file | Input file | Required
[-outfile] (Parameter 4) | outfile | Vienna RNAfold output file | Output file | <*>.ovrnacofoldconc
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
-aconstraintfile | infile | Vienna RNA structure constraints file (optional) | Input file | Required
-bconstraintfile | infile | Second vienna RNA structure constraints file (optional) | Input file | Required
-paramfile | infile | Vienna RNA parameters file (optional) | Input file | Required
-temperature | float | Temperature | Any numeric value | 37.0
-[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
-scale | float | Estimate of ensemble free energy | Any numeric value | 1.07
-dangles | list | Method |
0 | (Ignore)
1 | (Only unpaired bases for just one dangling end)
2 | (Always use dangling energies)
3 | (Allow coaxial stacking of adjacent helices)
| 1
-ssoutfile | outfile | Vienna structure postscript output file | Output file | <*>.ovrnacofoldconc
-aoutfile | outfile | First (a) vienna dotplot output file | Output file | <*>.ovrnacofoldconc
-aaoutfile | outfile | Second (a-a) vienna dotplot output file | Output file | <*>.ovrnacofoldconc
-boutfile | outfile | Third (b) vienna dotplot output file | Output file | <*>.ovrnacofoldconc
-bboutfile | outfile | Fourth (b-b) vienna dotplot output file | Output file | <*>.ovrnacofoldconc
-aboutfile | outfile | Fifth (a-b) vienna dotplot output file | Output file | <*>.ovrnacofoldconc
Associated qualifiers
"-asequence" associated sequence qualifiers
-sbegin1 -sbegin_asequence | integer | Start of the sequence to be used | Any integer value | 0
-send1 -send_asequence | integer | End of the sequence to be used | Any integer value | 0
-sreverse1 -sreverse_asequence | boolean | Reverse (if DNA) | Boolean value Yes/No | N
-sask1 -sask_asequence | boolean | Ask for begin/end/reverse | Boolean value Yes/No | N
-snucleotide1 -snucleotide_asequence | boolean | Sequence is nucleotide | Boolean value Yes/No | N
-sprotein1 -sprotein_asequence | boolean | Sequence is protein | Boolean value Yes/No | N
-slower1 -slower_asequence | boolean | Make lower case | Boolean value Yes/No | N
-supper1 -supper_asequence | boolean | Make upper case | Boolean value Yes/No | N
-scircular1 -scircular_asequence | boolean | Sequence is circular | Boolean value Yes/No | N
-squick1 -squick_asequence | boolean | Read id and sequence only | Boolean value Yes/No | N
-sformat1 -sformat_asequence | string | Input sequence format | Any string |
-iquery1 -iquery_asequence | string | Input query fields or ID list | Any string |
-ioffset1 -ioffset_asequence | integer | Input start position offset | Any integer value | 0
-sdbname1 -sdbname_asequence | string | Database name | Any string |
-sid1 -sid_asequence | string | Entryname | Any string |
-ufo1 -ufo_asequence | string | UFO features | Any string |
-fformat1 -fformat_asequence | string | Features format | Any string |
-fopenfile1 -fopenfile_asequence | string | Features file name | Any string |
"-bsequence" associated sequence qualifiers
-sbegin2 -sbegin_bsequence | integer | Start of the sequence to be used | Any integer value | 0
-send2 -send_bsequence | integer | End of the sequence to be used | Any integer value | 0
-sreverse2 -sreverse_bsequence | boolean | Reverse (if DNA) | Boolean value Yes/No | N
-sask2 -sask_bsequence | boolean | Ask for begin/end/reverse | Boolean value Yes/No | N
-snucleotide2 -snucleotide_bsequence | boolean | Sequence is nucleotide | Boolean value Yes/No | N
-sprotein2 -sprotein_bsequence | boolean | Sequence is protein | Boolean value Yes/No | N
-slower2 -slower_bsequence | boolean | Make lower case | Boolean value Yes/No | N
-supper2 -supper_bsequence | boolean | Make upper case | Boolean value Yes/No | N
-scircular2 -scircular_bsequence | boolean | Sequence is circular | Boolean value Yes/No | N
-squick2 -squick_bsequence | boolean | Read id and sequence only | Boolean value Yes/No | N
-sformat2 -sformat_bsequence | string | Input sequence format | Any string |
-iquery2 -iquery_bsequence | string | Input query fields or ID list | Any string |
-ioffset2 -ioffset_bsequence | integer | Input start position offset | Any integer value | 0
-sdbname2 -sdbname_bsequence | string | Database name | Any string |
-sid2 -sid_bsequence | string | Entryname | Any string |
-ufo2 -ufo_bsequence | string | UFO features | Any string |
-fformat2 -fformat_bsequence | string | Features format | Any string |
-fopenfile2 -fopenfile_bsequence | string | Features file name | Any string |
"-outfile" associated outfile qualifiers
-odirectory4 -odirectory_outfile | string | Output directory | Any string |
"-ssoutfile" associated outfile qualifiers
-odirectory | string | Output directory | Any string |
"-aoutfile" associated outfile qualifiers
-odirectory | string | Output directory | Any string |
"-aaoutfile" associated outfile qualifiers
-odirectory | string | Output directory | Any string |
"-boutfile" associated outfile qualifiers
-odirectory | string | Output directory | Any string |
"-bboutfile" associated outfile qualifiers
-odirectory | string | Output directory | Any string |
"-aboutfile" associated outfile qualifiers
-odirectory | 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

ovrnacofoldconc reads any normal sequence USAs.

### Input files for usage example

### File: cofold-red.fasta

    >red
    AUGAAGAUGA

### File: cofold-blue.fasta

    >blue
    CUGUCUGUCUUGAGACA

### File: cofold-conc.dat

    10 10

## Output file format

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

### Output files for usage example

### File: red.ovrnacofoldconc

    AUGAAGAUGA&CUGUCUGUCUUGAGACA
    ....((((..&..))))(((....))). ( -4.40)
    ....((((,.&..)))}(((....))). [ -5.88]
     frequency of mfe structure in ensemble 0.279848 , delta G binding= -1.57
    Free Energies:
    AB		AA		BB		A		B
    -5.838299	1.006546	-16.231717	-0.003662	-4.266495
    Kaa..0.193006 266048 12.7351
    Initial concentrations		relative Equilibrium concentrations
    A		 B		 AB		 AA		 BB		 A		 B
    10        	10        	0.01066 	0.14707 	0.24456 	0.19519 	0.00021

### Graphics File: red.ssps

### Graphics File: red.aps

### Graphics File: red.aaps

### Graphics File: red.abps

### Graphics File: red.bps

### Graphics File: red.bbps

## 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
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
ovrnaheat | Calculate specific heat of RNA melting
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