ovrnacofoldconc

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Function

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

Usage

% 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

Qualifier	Type	Description	Allowed values	Default
Standard (Mandatory) qualifiers
[-asequence] (Parameter 1)	sequence	Nucleotide sequence filename and optional format, or reference (input USA)	Readable sequence	Required
[-bsequence] (Parameter 2)	sequence	Nucleotide sequence filename and optional format, or reference (input USA)	Readable sequence	Required
[-concentrationfile] (Parameter 3)	infile	Vienna RNA concentration data file	Input file	Required
[-outfile] (Parameter 4)	outfile	Vienna RNAfold output file	Output file	<*>.ovrnacofoldconc
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
-aconstraintfile	infile	Vienna RNA structure constraints file (optional)	Input file	Required
-bconstraintfile	infile	Second vienna RNA structure constraints file (optional)	Input file	Required
-paramfile	infile	Vienna RNA parameters file (optional)	Input file	Required
-temperature	float	Temperature	Any numeric value	37.0
-[no]gu	boolean	Allow GU pairs	Boolean value Yes/No	Yes
-[no]closegu	boolean	Allow GU pairs at end of helices	Boolean value Yes/No	Yes
-[no]lp	boolean	Allow lonely pairs	Boolean value Yes/No	Yes
-[no]convert	boolean	Convert T to U	Boolean value Yes/No	Yes
-nsbases	string	Non-standard bases	Any string
-[no]tetraloop	boolean	Stabilizing energies for tetra-loops	Boolean value Yes/No	Yes
-energy	list	Rarely used option to fold sequences from the ABCD... alphabet	0 (BP) 1 (Any with GC) 2 (Any with AU parameters)	0
-scale	float	Estimate of ensemble free energy	Any numeric value	1.07
-dangles	list	Method	0 (Ignore) 1 (Only unpaired bases for just one dangling end) 2 (Always use dangling energies) 3 (Allow coaxial stacking of adjacent helices)	1
-ssoutfile	outfile	Vienna structure postscript output file	Output file	<*>.ovrnacofoldconc
-aoutfile	outfile	First (a) vienna dotplot output file	Output file	<*>.ovrnacofoldconc
-aaoutfile	outfile	Second (a-a) vienna dotplot output file	Output file	<*>.ovrnacofoldconc
-boutfile	outfile	Third (b) vienna dotplot output file	Output file	<*>.ovrnacofoldconc
-bboutfile	outfile	Fourth (b-b) vienna dotplot output file	Output file	<*>.ovrnacofoldconc
-aboutfile	outfile	Fifth (a-b) vienna dotplot output file	Output file	<*>.ovrnacofoldconc
Associated qualifiers
"-asequence" associated sequence qualifiers
-sbegin1 -sbegin_asequence	integer	Start of the sequence to be used	Any integer value	0
-send1 -send_asequence	integer	End of the sequence to be used	Any integer value	0
-sreverse1 -sreverse_asequence	boolean	Reverse (if DNA)	Boolean value Yes/No	N
-sask1 -sask_asequence	boolean	Ask for begin/end/reverse	Boolean value Yes/No	N
-snucleotide1 -snucleotide_asequence	boolean	Sequence is nucleotide	Boolean value Yes/No	N
-sprotein1 -sprotein_asequence	boolean	Sequence is protein	Boolean value Yes/No	N
-slower1 -slower_asequence	boolean	Make lower case	Boolean value Yes/No	N
-supper1 -supper_asequence	boolean	Make upper case	Boolean value Yes/No	N
-scircular1 -scircular_asequence	boolean	Sequence is circular	Boolean value Yes/No	N
-squick1 -squick_asequence	boolean	Read id and sequence only	Boolean value Yes/No	N
-sformat1 -sformat_asequence	string	Input sequence format	Any string
-iquery1 -iquery_asequence	string	Input query fields or ID list	Any string
-ioffset1 -ioffset_asequence	integer	Input start position offset	Any integer value	0
-sdbname1 -sdbname_asequence	string	Database name	Any string
-sid1 -sid_asequence	string	Entryname	Any string
-ufo1 -ufo_asequence	string	UFO features	Any string
-fformat1 -fformat_asequence	string	Features format	Any string
-fopenfile1 -fopenfile_asequence	string	Features file name	Any string
"-bsequence" associated sequence qualifiers
-sbegin2 -sbegin_bsequence	integer	Start of the sequence to be used	Any integer value	0
-send2 -send_bsequence	integer	End of the sequence to be used	Any integer value	0
-sreverse2 -sreverse_bsequence	boolean	Reverse (if DNA)	Boolean value Yes/No	N
-sask2 -sask_bsequence	boolean	Ask for begin/end/reverse	Boolean value Yes/No	N
-snucleotide2 -snucleotide_bsequence	boolean	Sequence is nucleotide	Boolean value Yes/No	N
-sprotein2 -sprotein_bsequence	boolean	Sequence is protein	Boolean value Yes/No	N
-slower2 -slower_bsequence	boolean	Make lower case	Boolean value Yes/No	N
-supper2 -supper_bsequence	boolean	Make upper case	Boolean value Yes/No	N
-scircular2 -scircular_bsequence	boolean	Sequence is circular	Boolean value Yes/No	N
-squick2 -squick_bsequence	boolean	Read id and sequence only	Boolean value Yes/No	N
-sformat2 -sformat_bsequence	string	Input sequence format	Any string
-iquery2 -iquery_bsequence	string	Input query fields or ID list	Any string
-ioffset2 -ioffset_bsequence	integer	Input start position offset	Any integer value	0
-sdbname2 -sdbname_bsequence	string	Database name	Any string
-sid2 -sid_bsequence	string	Entryname	Any string
-ufo2 -ufo_bsequence	string	UFO features	Any string
-fformat2 -fformat_bsequence	string	Features format	Any string
-fopenfile2 -fopenfile_bsequence	string	Features file name	Any string
"-outfile" associated outfile qualifiers
-odirectory4 -odirectory_outfile	string	Output directory	Any string
"-ssoutfile" associated outfile qualifiers
-odirectory	string	Output directory	Any string
"-aoutfile" associated outfile qualifiers
-odirectory	string	Output directory	Any string
"-aaoutfile" associated outfile qualifiers
-odirectory	string	Output directory	Any string
"-boutfile" associated outfile qualifiers
-odirectory	string	Output directory	Any string
"-bboutfile" associated outfile qualifiers
-odirectory	string	Output directory	Any string
"-aboutfile" associated outfile qualifiers
-odirectory	string	Output directory	Any string
General qualifiers
-auto	boolean	Turn off prompts	Boolean value Yes/No	N
-stdout	boolean	Write first file to standard output	Boolean value Yes/No	N
-filter	boolean	Read first file from standard input, write first file to standard output	Boolean value Yes/No	N
-options	boolean	Prompt for standard and additional values	Boolean value Yes/No	N
-debug	boolean	Write debug output to program.dbg	Boolean value Yes/No	N
-verbose	boolean	Report some/full command line options	Boolean value Yes/No	Y
-help	boolean	Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose	Boolean value Yes/No	N
-warning	boolean	Report warnings	Boolean value Yes/No	Y
-error	boolean	Report errors	Boolean value Yes/No	Y
-fatal	boolean	Report fatal errors	Boolean value Yes/No	Y
-die	boolean	Report dying program messages	Boolean value Yes/No	Y
-version	boolean	Report version number and exit	Boolean value Yes/No	N

Input file format

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

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

Graphics File: red.aps

Graphics File: red.aaps

Graphics File: red.abps

Graphics File: red.bps

Graphics File: red.bbps

Data files

Notes

References

Warnings

Diagnostic Error Messages

Exit status

Known bugs

See also

Author(s)

Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.

History

Target users

Comments