                               ovrnacofoldconc



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Function

   Calculate secondary structures of RNA dimers (concentrations)

Description

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

   It reads two RNA sequences wich are then allowed to form a dimer
   structure, calculates their minimum free energy (mfe) dimer structure
   and output the mfe structure in bracket notation and its free energy.
   It produces plots of the resulting secondary structure graph and a "dot
   plot" of the base pairing matrix. Since dimer formation is
   concentration dependent, it can be used to compute equilibrium
   concentrations for all five monomer and (homo/hetero)-dimer species,
   given input concentrations for the monomers.

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

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 ovrnacofoldconc


% ovrnacofoldconc
Calculate secondary structures of RNA dimers (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.ovrnacofoldconc]:


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

Command line arguments

Calculate secondary structures of RNA dimers (concentrations)
Version: EMBOSS:6.6.0.0

   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    [*.ovrnacofoldconc] 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))
   -ssoutfile          outfile    [*.ovrnacofoldconc] Vienna structure
                                  postscript output file
   -aoutfile           outfile    [*.ovrnacofoldconc] First (a) vienna dotplot
                                  output file
   -aaoutfile          outfile    [*.ovrnacofoldconc] Second (a-a) vienna
                                  dotplot output file
   -boutfile           outfile    [*.ovrnacofoldconc] Third (b) vienna dotplot
                                  output file
   -bboutfile          outfile    [*.ovrnacofoldconc] Fourth (b-b) vienna
                                  dotplot output file
   -aboutfile          outfile    [*.ovrnacofoldconc] 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
   -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

   "-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
   -scircular2         boolean    Sequence is circular
   -squick2            boolean    Read id and sequence only
   -sformat2           string     Input sequence format
   -iquery2            string     Input query fields or ID list
   -ioffset2           integer    Input start position offset
   -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

   ovrnacofoldconc 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

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

  Output files for usage example

  File: red.ovrnacofoldconc

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

   [ovrnacofoldconc results]

  Graphics File: red.aps

   [ovrnacofoldconc results]

  Graphics File: red.aaps

   [ovrnacofoldconc results]

  Graphics File: red.abps

   [ovrnacofoldconc results]

  Graphics File: red.bps

   [ovrnacofoldconc results]

  Graphics File: red.bbps

   [ovrnacofoldconc 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
   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
   ovrnaalifoldpf   Calculate secondary structures for a set of aligned RNAs
                    (partition)
   ovrnacofold      Calculate secondary structures of RNA dimers
   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
