                               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


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

   [ovrnaalifoldpf results]

  Graphics File: ecoli6s.ps

   [ovrnaalifoldpf results]

  Graphics File: ecoli6s.alirnaps

   [ovrnaalifoldpf results]

  File: ecoli6s.ovrnaalifoldpf

AUUUCCCUGAGGUGUUCGCCAGCGGGC_CAUGUCCCUGAGCCGAUAUUUAAUACCACAAGAAUGUGGUGCUCCGUGGUUG
GUGAGCAUGCUCGGCCCGU_______________CCGAGAAGCCUUAAAAUUGCGACGACACAUUCACCUUGAACCAA_G
GGUUCAAGGGCUACAGCCUGCAGCGGCA_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 (c) 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
