EMBASSY: VIENNA: ovrnaalifoldpf

| ovrnaalifoldpf

## Wiki

The master copies of EMBOSS documentation are available at http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki.

Please help by correcting and extending the Wiki pages.

## Function

Calculate secondary structures for a set of aligned RNAs (partition)

## Description

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

It reads aligned RNA sequences and calculates their minimum free energy (mfe) structure, partition function (pf) and base pairing probability matrix. It returns the mfe structure in bracket notation, its energy, the free energy of the thermodynamic ensemble and the frequency of the mfe structure in the ensemble. It also produces plots of the resulting secondary structure graph and a "dot plot" of the base pairing matrix.

The original program produces different outputs, depending on the options selected. In the EMBASSY implementation it is split into ovrnaalifold and ovrnaalifoldpf

## 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 ovrnaalifoldpf

    % ovrnaalifoldpf
    Calculate secondary structures for a set of aligned RNAs (partition)
    Input (aligned) nucleotide sequence set: ecoli6s.fasta
    Vienna RNAfold output file [ecoli6s.ovrnaalifoldpf]:

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

## Command line arguments

    Calculate secondary structures for a set of aligned RNAs (partition)
    Version: EMBOSS:6.6.0.0

       Standard (Mandatory) qualifiers:
      [-sequence]          seqset     (Aligned) nucleotide sequence set filename
                                      and optional format, or reference (input
                                      USA)
      [-outfile]           outfile    [*.ovrnaalifoldpf] Vienna RNAfold output
                                      file

       Additional (Optional) qualifiers: (none)
       Advanced (Unprompted) qualifiers:
       -constraintfile     infile     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
       -circular           boolean    [N] Circular RNA
       -colour             boolean    [N] Colour structure plot
       -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       [2] 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))
       -covariance         float      [1.0] Weight for covariance (Any numeric
                                      value)
       -nspenalty          float      [1.0] Non-compatible sequence penalty (Any
                                      numeric value)
       -endgaps            boolean    [N] Mark end gaps
       -most               boolean    [N] Use most informative sequence algorithm
       -dotoutfile         outfile    [*.ovrnaalifoldpf] Vienna dotplot postscript
                                      output file (optional)
       -ssoutfile          outfile    [*.ovrnaalifoldpf] Vienna RNA structure
                                      postscript output file
       -alignoutfile       outfile    [*.ovrnaalifoldpf] Vienna RNA alignment
                                      postscript output file (optional)

       Associated qualifiers:

       "-sequence" associated qualifiers
       -sbegin1            integer    Start of each sequence to be used
       -send1              integer    End of each 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

       "-dotoutfile" associated qualifiers
       -odirectory         string     Output directory

       "-ssoutfile" associated qualifiers
       -odirectory         string     Output directory

       "-alignoutfile" 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
[-sequence] (Parameter 1) | seqset | (Aligned) nucleotide sequence set filename and optional format, or reference (input USA) | Readable set of sequences | Required
[-outfile] (Parameter 2) | outfile | Vienna RNAfold output file | Output file | <*>.ovrnaalifoldpf
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
-constraintfile | infile | 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
-circular | boolean | Circular RNA | Boolean value Yes/No | No
-colour | boolean | Colour structure plot | Boolean value Yes/No | No
-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)
| 2
-covariance | float | Weight for covariance | Any numeric value | 1.0
-nspenalty | float | Non-compatible sequence penalty | Any numeric value | 1.0
-endgaps | boolean | Mark end gaps | Boolean value Yes/No | No
-most | boolean | Use most informative sequence algorithm | Boolean value Yes/No | No
-dotoutfile | outfile | Vienna dotplot postscript output file (optional) | Output file | <*>.ovrnaalifoldpf
-ssoutfile | outfile | Vienna RNA structure postscript output file | Output file | <*>.ovrnaalifoldpf
-alignoutfile | outfile | Vienna RNA alignment postscript output file (optional) | Output file | <*>.ovrnaalifoldpf
Associated qualifiers
"-sequence" associated seqset qualifiers
-sbegin1 -sbegin_sequence | integer | Start of each sequence to be used | Any integer value | 0
-send1 -send_sequence | integer | End of each 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 |
"-dotoutfile" associated outfile qualifiers
-odirectory | string | Output directory | Any string |
"-ssoutfile" associated outfile qualifiers
-odirectory | string | Output directory | Any string |
"-alignoutfile" 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

ovrnaalifoldpf reads any normal sequence USAs.

### Input files for usage example

### File: ecoli6s.fasta

    >X01238.1/1-183
    AUUUCUCUGAGAUGUUCGCAAGCGGGC.CAGUCCCCUGAGCCGAUAUUUCAUACCACAAG
    AAUGUGGCGCUCCGCGGUUGGUGAGCAUGCUCGGUCCGU...............CCGAGA
    AGCCUUAAAACUGCGACGACACAUUCACCUUGAACCAA.GGGUUCAAGGGUUACAGCCUG
    CGGCGGCA.UC.UCGGAG.AUUC
    >AL627277.1/108623-108805
    AUUUCUCUGAGAUGUUUGCAAGCGGGC.CAGUCCCCUGAGCCGAUAUUUCAUACCACAAG
    AAUGUGGCGCUCCGCGGUUGGUGAGCAUGCUCGGUUCGU...............CCGAGA
    AGCCUUAAAACUGUGACGACACAUUCACCUUGAACCAA.GGGUUCAAGGGUUACAGCCUG
    CGGCGGCA.UC.UCGGAG.AUUC
    >AJ414145.1/90993-91174
    AUUUCUCUGAGGUGUUUGCCAGCGGGC.CAGUCCCCUGAGCCGAUAUUUAAUACCAACAG
    AAUGUAGUGCUCCGUAACCGGUGAGCAUGCUCGGUCCG................CCGAGA
    AGCCUUAAGGUUGCGACGCUGCGUUCACCUUGAACCAA.GGGUUCAAGGGUUACAGCCUG
    CGACGGCA.CC.UCGGAG.AUCC
    >U32767.1/6538-6734
    .AUUACCUGGAGUGUUCGUCAGUAGGC.UAUGUCCCUGAGCCGAUACUUUAAAUCUUAUA
    AAUU.GGUUUCCUAUCGUUGGUGUGUAGGCUUAACCUUUGACUCGUUCAUUGGGCUAAGA
    AACCUGAAAACGGUAUCAACUGAUUU.CCUUGAACCGUCGGGUUCAAGGACUACUGCCCG
    CAGCGGCACUC.UGGGGU.CUUC
    >AE006208.1/8365-8185
    .AUUACCUGAGGUGUUUGCCAGUGGGU.UAUGUCCCUGAGCCGAUACUUU.UAUUUUAUG
    AAUC.GGUUUCUAAUUGUUGGUGUGCAUGCUUAGCUUGA...............CUAAGA
    AGCCUAAAAAUAGUUAUAACUGAUUC.CCUUGAACCGUUGGGUUCAAGGACUGAGACUUG
    CAGCGGCA.UC.UCGGGUUCUUC
    >Y00334.1/77-254
    CGCUCCCUGGUGUGUUGGCCAGUCGGU.GAUGUCCCUGAGCCGAUAACUGCAACAAC..G
    GAGGUUGC.CAGUUGGACCGGUGUGCAUGUCCGCACG.................ACGGAA
    AGCCUUAAGGUCUAC.UGCAACCGCCACCUUGAACUUUCGGGUUCAAGGGCUA.ACCCGA
    CAGCGGCA.CGACCGGGG.AGCU
    >AE004317.1/5626-5807
    UUUACCCUGGGGUGUUCGUCAGCGGAUUUAUGUCCCUGAGCCGAUAAGCAACAUAAC..A
    GGGUUGGUAUUGGGUAGCUAUUGAGCAAGCUCGGCUUGUA..............CCGAGA
    AGCCUGCGGUUACCAUUACUGAUCCG.CCUUGAACCUGAUGGUUCAAGGGCUACGAUCCU
    CAACGGCA.UC.CCGGGG.UUC.

## Output file format

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

### Output files for usage example

### Graphics File: ecoli6s.ssps

### Graphics File: ecoli6s.ps

### Graphics File: ecoli6s.alirnaps

### File: ecoli6s.ovrnaalifoldpf

    AUUUCCCUGAGGUGUUCGCCAGCGGGC_CAUGUCCCUGAGCCGAUAUUUAAUACCACAAGAAUGUGGUGCUCCGUGGUUGGUGAGCAUGCUCGGCCCGU_______________CCGAGAAGCCUUAAAAUUGCGACGACACAUUCACCUUGAACCAA_GGGUUCAAGGGCUACAGCCUGCAGCGGCA_UC_UCGGGG_AUUC
    ....(((((((((((.(((..((((((................................(((((((......(((((((...(.((...(((((....................)))))..)))....)))))))....))))))).(((((((((....)))))))))......)))))).)))))).)).))))))..... (-56.91 = -48.71 +  -8.20)
    ....(((((((((({{(((..((((((................................(((((((......(((((((...{.((...(((((....................)))))..)),....)))))))..,.))))))).(((((((((....)))))))))......)))))).)))))).)).))))))..... [-59.30]
     frequency of mfe structure in ensemble 0.0206905

    # Alignment section

    7 sequences; length of alignment 203
    alifold output
       64   142  0 100.0%   0.000 CG:1    GC:4    UG:1    UA:1
       63   143  0  99.9%   0.002 GC:1    GU:1    UG:1    UA:4
       74   134  0  99.8%   0.005 GC:3    GU:1    AU:2    UA:1
       77   131  0 100.0%   0.001 GC:3    GU:2    AU:2
       10   193  0  99.8%   0.006 GC:2    GU:1    AU:4
       76   132  1  99.9%   0.003 CG:1    GC:1    GU:2    AU:1    UA:1
       79   129  0  99.3%   0.032 CG:2    UG:1    UA:4
       66   140  0  98.3%   0.056 GC:4    GU:1    AU:1    UA:1
       92   117  0 100.0%   0.000 CG:5    UA:2
       91   118  0 100.0%   0.001 CG:1    UA:6
        6   197  0 100.0%   0.001 CG:4    UA:3
       90   119  0  99.9%   0.003 CG:6    UA:1
       61   145  0  99.8%   0.005 GC:2    AU:5
       93   116  0  99.8%   0.007 GC:5    AU:2
       75   133  1  99.9%   0.003 CG:2    GU:1    UG:3
        7   196  0 100.0%   0.000 CG:7
       78   130  1  99.9%   0.010 CG:2    UA:4
        8   195  0  99.8%   0.007 UG:7
       62   144  1  99.7%   0.010 GC:1    AU:5
        9   194  1  99.9%   0.003 GC:6
       86   122  0  98.0%   0.083 CG:6    UA:1
       65   141  2  99.1%   0.028 UG:2    UA:3
       60   146  1  98.4%   0.050 GC:5    AU:1
      152   165  0  98.0%   0.170 GC:7
      155   162  0  98.0%   0.170 CG:7
       85   123  0  97.9%   0.102 GC:7
      153   164  0  97.9%   0.141 AU:7
      154   163  0  97.9%   0.142 AU:7
      151   166  0  97.5%   0.170 UA:7
        5   198  0  96.3%   0.110 CG:5    AU:2
      150   167  0  96.2%   0.158 UA:7
       25   178  0  95.2%   0.329 GC:6    GU:1
       26   177  0  95.1%   0.319 GC:6    AU:1
       23   180  1  95.0%   0.199 CG:3    UG:2    UA:1
       24   179  1  95.0%   0.320 CG:1    GC:1    GU:4
       22   181  0  93.7%   0.311 GC:7
      149   168  0  93.7%   0.404 CG:7
      156   161  0  92.4%   0.322 CG:6    UG:1
       27   176  1  91.6%   0.277 CG:4    UA:2
       18   184  0  90.9%   0.490 GC:7
       73   135  2  88.8%   0.331 CG:3    AU:1    UA:1

      [Part of this file has been deleted for brevity]

       25    36  0   0.6%   0.518 GC:7    +
       24    37  1   0.6%   0.725 GU:5    AU:1    +
       85   124  0   0.3%   0.462 GC:7    +
      101   107  0   0.3%   0.080 AU:1    --:6    +
       16   188  0   0.3%   0.831 UA:7    +
      102   114  0   0.2%   0.070 CG:1    --:6    +
      103   113  0   0.2%   0.070 UG:1    --:6    +
      104   112  0   0.2%   0.052 CG:1    --:6    +
       34    38  0   0.2%   0.894 CG:7    +
       16    25  0   0.2%   0.927 UG:7    +
      101   110  0   0.2%   0.061 AU:1    --:6    +
       34    43  0   0.2%   0.658 CG:7    +
       38    42  0   0.2%   0.938 GC:7    +
       37    43  0   0.1%   0.727 UG:7    +
      105   111  0   0.1%   0.030 GU:1    --:6    +
      101   106  0   0.1%   0.063 AU:1    --:6    +
      148   152  0   0.1%   0.237 CG:7    +
       35    43  0   0.1%   0.641 CG:7    +
       25    35  0   0.1%   0.629 GC:7    +
       84   126  2   0.1%   0.039 UG:1    AU:3    UA:1    +
      103   114  0   0.1%   0.071 UG:1    --:6    +
      107   114  0   0.1%   0.072 UG:1    --:6    +
       36   169  0   0.1%   0.882 CG:7    +
      156   160  1   0.1%   0.158 CG:5    UG:1    +
      104   113  0   0.1%   0.058 CG:1    --:6    +
       15   188  0   0.1%   0.501 UA:7    +
       35    40  0   0.1%   0.939 CG:7    +
      155   160  1   0.5%   0.136 CG:6    +
       26    35  1   0.5%   0.639 GC:6    +
       81   126  2   0.2%   0.101 GU:4    UG:1    +
       40    47  2   0.2%   0.584 GC:2    GU:3    +
       81   123  1   0.4%   0.129 GC:6    +
       80   124  1   0.4%   0.460 GC:6    +
      151   157  2   0.2%   0.073 UG:2    UA:3    +
       70   135  2   0.2%   0.499 CG:3    UA:2    +
       82   127  1   0.3%   0.077 UA:6    +
       81   125  1   0.3%   0.339 GU:6    +
       19   182  2   0.1%   0.249 CG:3    UA:2    +
       67    72  2   0.1%   0.036 GC:4    GU:1    +
       79   128  2   0.1%   0.028 UG:1    UA:4    +
       81   124  1   0.2%   0.483 GC:6    +
      149   160  1   0.2%   0.141 CG:6    +
       14   191  1   0.1%   0.284 GC:6    +
       26    34  1   0.1%   0.634 GC:6    +
      148   160  1   0.1%   0.241 CG:6    +
       44    49  1   0.1%   0.062 AU:6    +
       39    48  2   0.2%   0.416 AU:5    +
       35   170  2   0.2%   1.006 CG:5    +
       24    36  2   0.1%   0.486 GC:5    +
       20    25  2   0.1%   0.419 CG:5    +
    ....(((((((((({{(((..((((((................................(((((((......(((((((...{.((...(((((....................)))))..)),....)))))))..,.))))))).(((((((((....)))))))))......)))))).)))))).)).)))))).....

## 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
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
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