                                vrnaalifoldpf



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Function

   RNA alignment folding with partition

Description

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

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

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 vrnaalifoldpf


% vrnaalifoldpf
RNA alignment folding with partition
Input (aligned) nucleotide sequence set: ecoli6s.fasta
Vienna RNAfold output file [ecoli6s.vrnaalifoldpf]:


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

Command line arguments

RNA alignment folding with partition
Version: EMBOSS:6.2.0

   Standard (Mandatory) qualifiers:
  [-sequence]          seqset     (Aligned) nucleotide sequence set filename
                                  and optional format, or reference (input
                                  USA)
  [-outfile]           outfile    [*.vrnaalifoldpf] 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    [*.vrnaalifoldpf] Vienna dotplot postscript
                                  output file (optional)
   -ssoutfile          outfile    [*.vrnaalifoldpf] Vienna RNA structure
                                  postscript output file
   -alignoutfile       outfile    [*.vrnaalifoldpf] 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
   -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

   "-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

   vrnaalifoldpf 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

   vrnaalifoldpf 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

   [vrnaalifoldpf results]

  Graphics File: ecoli6s.ps

   [vrnaalifoldpf results]

  Graphics File: ecoli6s.alirnaps

   [vrnaalifoldpf results]

  File: ecoli6s.vrnaalifoldpf

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
                    einverted      Finds inverted repeats in nucleotide sequences
                    vrnaalifold    RNA alignment folding
                    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
                    vrnaheat       RNA melting
                    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.

Comments
