
                              vrnacofoldconc 



Function

   RNA cofolding with concentrations

Description

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

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

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 vrnacofoldconc


% vrnacofoldconc 
RNA cofolding with 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.vrnacofoldconc]: 

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

Command line arguments

   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    [*.vrnacofoldconc] Vienna RNAfold output
                                  file

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers:
   -aconstraintfile    infile     Vienna RNA structure contraints file
                                  (optional)
   -bconstraintfile    infile     Second vienna RNA structure contraints 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 is accepted)
   -[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))
   -paired             boolean    [N] Calculate probabilities of base pairing
   -ssoutfile          outfile    [*.vrnacofoldconc] Output file name
   -aoutfile           outfile    [*.vrnacofoldconc] First (a) vienna dotplot
                                  output file
   -aaoutfile          outfile    [*.vrnacofoldconc] Second (a-a) vienna
                                  dotplot output file
   -boutfile           outfile    [*.vrnacofoldconc] Third (b) vienna dotplot
                                  output file
   -bboutfile          outfile    [*.vrnacofoldconc] Fourth (b-b) vienna
                                  dotplot output file
   -aboutfile          outfile    [*.vrnacofoldconc] 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
   -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

   "-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
   -sformat2           string     Input sequence format
   -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 standard output
   -filter             boolean    Read standard input, write 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. 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

Input file format

   vrnacofoldconc 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

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

  Output files for usage example

  File: red.vrnacofoldconc

AUGAAGAUGA&CUGUCUGUCUUGAGACA
....((((..&..))))(((....))). ( -4.40)
Expinit2 = 0.513986
tab = -1.738299 taa = 4.679345  tbb = -12.558919

Free Energies:
    AB          AA              BB              A               B
-5.884889       -0.208509       -16.658920      -0.003662       -4.266495

Initial concentrations          Equilibrium concentrations
A                B                      AB               AA              BB
         A               B
10.000000       10.000000               0.844630        3.676596        4.49106
2       1.802178        0.173246 f
10.000000       10.000000               0.042232        0.183830        0.22455
3       0.090109        0.008662 f
....((((,...)))}(((....))). [ -5.88]
 frequency of mfe structure in ensemble 0.279849

  File: red.ssps

%!PS-Adobe-3.0 EPSF-3.0
%%Creator: ePS_dot.c,v 1.1 2005/10/13 13:00:44 ajb Exp $, ViennaRNA-1.6
%%CreationDate: Sat Jul 15 12:00:00 2006
%%Title: Rna secondary Structure Plot
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%%Pages: 1
%%EndComments

%Options:
% to switch off outline pairs of sequence comment or
% delete the appropriate line near the end of the file

%%BeginProlog
/RNAplot 100 dict def
RNAplot begin
/fsize  14 def
/outlinecolor {0.2 setgray} bind def
/paircolor    {0.2 setgray} bind def
/seqcolor     {0   setgray} bind def
/cshow  { dup stringwidth pop -2 div fsize -3 div rmoveto show} bind def
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  stroke
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% draw bases
/drawbases {
  [] 0 setdash
  seqcolor
  0
  coor {
    aload pop moveto
    dup sequence exch 1 getinterval cshow
    1 add


  [Part of this file has been deleted for brevity]

AUGAAGAUGACUGUCUGUCUUGAGACA\
) def
/coor [
[96.276 111.415]
[91.331 110.049]
[86.992 106.486]
[84.234 101.044]
[83.858 94.465]
[73.252 83.858]
[62.645 73.252]
[52.039 62.645]
[36.067 58.926]
[31.562 43.157]
[43.157 31.562]
[58.926 36.067]
[62.645 52.039]
[73.252 62.645]
[83.858 73.252]
[94.465 83.858]
[107.979 90.367]
[122.885 92.046]
[137.791 93.726]
[152.597 86.675]
[165.951 96.194]
[164.115 112.490]
[148.978 118.799]
[136.111 108.631]
[121.206 106.952]
[106.300 105.272]
[104.357 108.419]
] def
/pairs [
[5 16]
[6 15]
[7 14]
[8 13]
[17 26]
[18 25]
[19 24]
] def

init

% switch off outline pairs or bases by removing these lines
drawoutline
drawpairs
drawbases
% show it
showpage
end
%%EOF

  File: red.aps

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%
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%This file contains the square roots of the base pair probabilities in the form
% i  j  sqrt(p(i,j)) ubox

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   3 1 roll
   exch len exch sub 1 add box
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/lbox {
   3 1 roll
   len exch sub 1 add box
} bind def

/drawseq {
% print sequence along all 4 sides
[ [0.7 -0.3 0 ]
  [0.7 0.7 len add 0]
  [-0.3 len sub -0.4 -90]


  [Part of this file has been deleted for brevity]

     len lineto
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  [] 0 setdash
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    len exch sub dup
    -1 exch moveto len 1 add exch lineto
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  0.5 neg dup translate
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end
%%EndProlog
DPdict begin
%delete next line to get rid of title
270 665 moveto /Helvetica findfont 14 scalefont setfont (red.aps) show

/sequence { (\
AUGAAGAUGA\
) } def
/len { sequence length } bind def

72 216 translate
72 6 mul len 1 add div dup scale
/Helvetica findfont 0.95 scalefont setfont

drawseq
0.5 dup translate
% draw diagonal
0.04 setlinewidth
0 len moveto len 0 lineto stroke

drawgrid
%data starts here
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end
%%EOF

  File: red.aaps

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%Options: -d2
%
%FreeEnergy= -0.208508983

%This file contains the square roots of the base pair probabilities in the form
% i  j  sqrt(p(i,j)) ubox

%%BeginProlog
/DPdict 100 dict def
DPdict begin
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/lbox {
   3 1 roll
   len exch sub 1 add box
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/drawseq {
% print sequence along all 4 sides
[ [0.7 -0.3 0 ]
  [0.7 0.7 len add 0]
  [-0.3 len sub -0.4 -90]


  [Part of this file has been deleted for brevity]

0 len moveto len 0 lineto stroke

drawgrid
%data starts here
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end
%%EOF

  File: red.abps

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%Options: -d2
%
%FreeEnergy= -5.884888649

%This file contains the square roots of the base pair probabilities in the form
% i  j  sqrt(p(i,j)) ubox

%%BeginProlog
/DPdict 100 dict def
DPdict begin
/logscale false def
/box { %size x y box - draws box centered on x,y
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/lbox {
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   len exch sub 1 add box
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/drawseq {
% print sequence along all 4 sides
[ [0.7 -0.3 0 ]
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  [-0.3 len sub -0.4 -90]


  [Part of this file has been deleted for brevity]

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%%EOF

  File: red.bps

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%Options: -d2
%
%FreeEnergy= -4.266494751

%This file contains the square roots of the base pair probabilities in the form
% i  j  sqrt(p(i,j)) ubox

%%BeginProlog
/DPdict 100 dict def
DPdict begin
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% print sequence along all 4 sides
[ [0.7 -0.3 0 ]
  [0.7 0.7 len add 0]
  [-0.3 len sub -0.4 -90]


  [Part of this file has been deleted for brevity]

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%%EndProlog
DPdict begin
%delete next line to get rid of title
270 665 moveto /Helvetica findfont 14 scalefont setfont (red.bps) show

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CUGUCUGUCUUGAGACA\
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%data starts here
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end
%%EOF

  File: red.bbps

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%Options: -d2
%
%FreeEnergy= -16.658920288

%This file contains the square roots of the base pair probabilities in the form
% i  j  sqrt(p(i,j)) ubox

%%BeginProlog
/DPdict 100 dict def
DPdict begin
/logscale false def
/box { %size x y box - draws box centered on x,y
   2 index 0.5 mul add            % x += 0.5
   exch 2 index 0.5 mul add exch  % x += 0.5
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/ubox {
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   } if
   3 1 roll
   exch len exch sub 1 add box
} bind def

/lbox {
   3 1 roll
   len exch sub 1 add box
} bind def

/drawseq {
% print sequence along all 4 sides
[ [0.7 -0.3 0 ]
  [0.7 0.7 len add 0]
  [-0.3 len sub -0.4 -90]


  [Part of this file has been deleted for brevity]

/cutpoint 18 def

72 216 translate
72 6 mul len 1 add div dup scale
/Helvetica findfont 0.95 scalefont setfont

drawseq
0.5 dup translate
% draw diagonal
0.04 setlinewidth
0 len moveto len 0 lineto stroke

drawgrid
%data starts here
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showpage
end
%%EOF

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 DNA inverted repeats
   vrnaalifold   RNA alignment folding
   vrnaalifoldpf RNA alignment folding with partition
   vrnacofold    RNA cofolding
   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
