                               vrnacofoldconc



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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

RNA cofolding with concentrations
Version: EMBOSS:6.2.0

   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    [*.vrnacofoldconc] 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))
   -paired             boolean    [N] Calculate probabilities of base pairing
   -ssoutfile          outfile    [*.vrnacofoldconc] Vienna structure
                                  postscript output file
   -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 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

   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)
....((((,.&..)))}(((....))). [ -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

   [vrnacofoldconc results]

  Graphics File: red.aps

   [vrnacofoldconc results]

  Graphics File: red.aaps

   [vrnacofoldconc results]

  Graphics File: red.abps

   [vrnacofoldconc results]

  Graphics File: red.bps

   [vrnacofoldconc results]

  Graphics File: red.bbps

   [vrnacofoldconc results]

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
   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
