EMBASSY: VIENNA: vrnacofoldpf

vrnacofoldpf

Wiki

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Function

RNA cofolding with partitioning

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. It also computes the partition function (pf) and base pairing probability matrix.

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 vrnacofoldpf

% vrnacofoldpf RNA cofolding with partitioning Input nucleotide sequence: cofold-red.fasta Second nucleotide sequence: cofold-blue.fasta Vienna RNAfold output file [red.vrnacofoldpf]:

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

Command line arguments

RNA cofolding with partitioning
Version: EMBOSS:6.4.0.0

   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)
  [-outfile]           outfile    [*.vrnacofoldpf] 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       [2] 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    [*.vrnacofoldpf] Vienna structure postscript
                                  output file
   -dotoutfile         outfile    [*.vrnacofoldpf] Vienna dotplot postscript
                                  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
   -odirectory3        string     Output directory

   "-ssoutfile" associated qualifiers
   -odirectory         string     Output directory

   "-dotoutfile" 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

[-outfile]
(Parameter 3) outfile Vienna RNAfold output file Output file <*>.vrnacofoldpf

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)
2

-ssoutfile outfile Vienna structure postscript output file Output file <*>.vrnacofoldpf

-dotoutfile outfile Vienna dotplot postscript output file Output file <*>.vrnacofoldpf

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

-sformat1
-sformat_asequence string Input sequence format Any string

-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

-sformat2
-sformat_bsequence string Input sequence format Any string

-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

-odirectory3
-odirectory_outfile string Output directory Any string

"-ssoutfile" associated outfile qualifiers

-odirectory string Output directory Any string

"-dotoutfile" 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

vrnacofoldpf reads any normal sequence USAs.

Input files for usage example

File: cofold-red.fasta

>red
AUGAAGAUGA

File: cofold-blue.fasta

>blue
CUGUCUGUCUUGAGACA

Output file format

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

Output files for usage example

File: red.vrnacofoldpf

AUGAAGAUGA&CUGUCUGUCUUGAGACA
..........&.(((((......))))) ( -4.70)
.,.,((({,.&..,|||}}}},.},,,. [ -5.57]
 frequency of mfe structure in ensemble 0.242781 , delta G binding= -0.46

Graphics File: red.ps

[vrnacofoldpf results]

Graphics File: red.ssps

[vrnacofoldpf 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.

Program name	Description
banana	Plot bending and curvature data for B-DNA
btwisted	Calculate the twisting in a B-DNA sequence
einverted	Finds inverted repeats in nucleotide sequences
ovrnaalifold	RNA alignment folding
ovrnaalifoldpf	RNA alignment folding with partition
ovrnacofold	RNA cofolding
ovrnacofoldconc	RNA cofolding with concentrations
ovrnacofoldpf	RNA cofolding with partitioning
ovrnadistance	RNA distances
ovrnaduplex	RNA duplex calculation
ovrnaeval	RNA eval
ovrnaevalpair	RNA eval with cofold
ovrnafold	Calculate secondary structures of RNAs
ovrnafoldpf	Secondary structures of RNAs with partition
ovrnaheat	RNA melting
ovrnainverse	RNA sequences matching a structure
ovrnalfold	Calculate locally stable secondary structures of RNAs
ovrnaplot	Plot vrnafold output
ovrnasubopt	Calculate RNA suboptimals
sirna	Finds siRNA duplexes in mRNA
vrna2dfold	Structures and samples of k,l neighbourhoods
vrnaaliduplex	RNA duplex calculation for two sequence alignments
vrnaalifold	RNA alignment folding
vrnaalifoldpf	RNA alignment folding with partition
vrnacofold	RNA cofolding
vrnacofoldconc	RNA cofolding with concentrations
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
vrnalalifoldpf	Locally stable 2ry structures for a set of aligned RNAs
vrnalfold	Calculate locally stable secondary structures of RNAs
vrnalfoldz	Locally stable secondary structures of RNAs plus zscore
vrnapkplex	RNA structures plus pseudoknots
vrnaplfold	Locally stable RNA 2ry structures - pair probabilities
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.

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.

Wiki

Function

Description

Algorithm

Usage

Command line arguments

Input file format

Input files for usage example

File: cofold-red.fasta

File: cofold-blue.fasta

Output file format

Output files for usage example

File: red.vrnacofoldpf

Graphics File: red.ps

Graphics File: red.ssps

Data files

Notes

References

Warnings

Diagnostic Error Messages

Exit status

Known bugs

See also

Author(s)

History

Target users

Comments