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 

   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 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] 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. 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

Standard (Mandatory) qualifiers Allowed values Default
[-asequence]
(Parameter 1)		 Nucleotide sequence filename and optional format, or reference (input USA) Readable sequence Required
[-bsequence]
(Parameter 2)		 Nucleotide sequence filename and optional format, or reference (input USA) Readable sequence Required
[-concentrationfile]
(Parameter 3)		 Vienna RNA concentration data file Input file Required
[-outfile]
(Parameter 4)		 Vienna RNAfold output file Output file <*>.vrnacofoldconc
Additional (Optional) qualifiers Allowed values Default
(none)
Advanced (Unprompted) qualifiers Allowed values Default
-aconstraintfile Vienna RNA structure constraints file (optional) Input file Required
-bconstraintfile Second vienna RNA structure constraints file (optional) Input file Required
-paramfile Vienna RNA parameters file (optional) Input file Required
-temperature Temperature Any numeric value 37.0
-[no]gu Allow GU pairs Boolean value Yes/No Yes
-[no]closegu Allow GU pairs at end of helices Boolean value Yes/No Yes
-[no]lp Allow lonely pairs Boolean value Yes/No Yes
-[no]convert Convert T to U Boolean value Yes/No Yes
-nsbases Non-standard bases Any string is accepted An empty string is accepted
-[no]tetraloop Stabilizing energies for tetra-loops Boolean value Yes/No Yes
-energy Rarely used option to fold sequences from the ABCD... alphabet
0 (BP)
1 (Any with GC)
2 (Any with AU parameters)
 0
-scale Estimate of ensemble free energy Any numeric value 1.07
-dangles 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
-paired Calculate probabilities of base pairing Boolean value Yes/No No
-ssoutfile Vienna structure postscript output file Output file <*>.vrnacofoldconc
-aoutfile First (a) vienna dotplot output file Output file <*>.vrnacofoldconc
-aaoutfile Second (a-a) vienna dotplot output file Output file <*>.vrnacofoldconc
-boutfile Third (b) vienna dotplot output file Output file <*>.vrnacofoldconc
-bboutfile Fourth (b-b) vienna dotplot output file Output file <*>.vrnacofoldconc
-aboutfile Fifth (a-b) vienna dotplot output file Output file <*>.vrnacofoldconc

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