vrnaevalpair

 

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Function

RNA eval with cofold

Description

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

It evaluates the free energy of the co-folding of two RNA strands with fixed secondary structure. Sequences and structures are read and the energy in Kcal/Mol is output.

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

Algorithm

The program will continue to read new sequences and structures until a line consisting of the single character "@" or an end of file condition is encountered.

See the original documentation for the Vienna RNA package http://www.tbi.univie.ac.at/~ivo/RNA/

Usage

Here is a sample session with vrnaevalpair


% vrnaevalpair 
RNA eval with cofold
Input nucleotide sequence: cofold-red.fasta
Vienna RNA structure constraints file: cofold-red.con
Second nucleotide sequence: cofold-blue.fasta
Second vienna RNA structure constraints file: cofold-blue.con
Vienna RNAeval output file [red.vrnaevalpair]: 

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

Command line arguments

RNA eval with cofold
Version: EMBOSS:6.4.0.0

   Standard (Mandatory) qualifiers:
  [-asequence]         sequence   Nucleotide sequence filename and optional
                                  format, or reference (input USA)
  [-aconstraintfile]   infile     Vienna RNA structure constraints file
  [-bsequence]         sequence   Nucleotide sequence filename and optional
                                  format, or reference (input USA)
  [-bconstraintfile]   infile     Second vienna RNA structure constraints file
  [-outfile]           outfile    [*.vrnaevalpair] Vienna RNAeval output file

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers:
   -paramfile          infile     Vienna RNA parameters file (optional)
   -temperature        float      [37.0] Temperature (Any numeric value)
   -[no]convert        boolean    [Y] Convert T to U
   -[no]tetraloop      boolean    [Y] Stabilising energies for tetra-loops
   -circular           boolean    [N] Circular RNA
   -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))
   -dangles            menu       [2] Method (Values: 0 (No stabilising
                                  energies for dangling ends); 1 (Use
                                  stabilising energies for dangling ends); 2
                                  (Dangling energies as in a partition
                                  function 3:Allow coaxial stacking of
                                  adjacent helices))
   -logml              boolean    [N] Use log scale for multiloop energies

   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
   -sbegin3            integer    Start of the sequence to be used
   -send3              integer    End of the sequence to be used
   -sreverse3          boolean    Reverse (if DNA)
   -sask3              boolean    Ask for begin/end/reverse
   -snucleotide3       boolean    Sequence is nucleotide
   -sprotein3          boolean    Sequence is protein
   -slower3            boolean    Make lower case
   -supper3            boolean    Make upper case
   -sformat3           string     Input sequence format
   -sdbname3           string     Database name
   -sid3               string     Entryname
   -ufo3               string     UFO features
   -fformat3           string     Features format
   -fopenfile3         string     Features file name

   "-outfile" associated qualifiers
   -odirectory5        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
[-aconstraintfile]
(Parameter 2)
infile Vienna RNA structure constraints file Input file Required
[-bsequence]
(Parameter 3)
sequence Nucleotide sequence filename and optional format, or reference (input USA) Readable sequence Required
[-bconstraintfile]
(Parameter 4)
infile Second vienna RNA structure constraints file Input file Required
[-outfile]
(Parameter 5)
outfile Vienna RNAeval output file Output file <*>.vrnaevalpair
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
-paramfile infile Vienna RNA parameters file (optional) Input file Required
-temperature float Temperature Any numeric value 37.0
-[no]convert boolean Convert T to U Boolean value Yes/No Yes
-[no]tetraloop boolean Stabilising energies for tetra-loops Boolean value Yes/No Yes
-circular boolean Circular RNA Boolean value Yes/No No
-energy list Rarely used option to fold sequences from the ABCD... alphabet
0 (BP)
1 (Any with GC)
2 (Any with AU parameters)
0
-dangles list Method
0 (No stabilising energies for dangling ends)
1 (Use stabilising energies for dangling ends)
2 (Dangling energies as in a partition function 3:Allow coaxial stacking of adjacent helices)
2
-logml boolean Use log scale for multiloop energies Boolean value Yes/No No
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
-sbegin3
-sbegin_bsequence
integer Start of the sequence to be used Any integer value 0
-send3
-send_bsequence
integer End of the sequence to be used Any integer value 0
-sreverse3
-sreverse_bsequence
boolean Reverse (if DNA) Boolean value Yes/No N
-sask3
-sask_bsequence
boolean Ask for begin/end/reverse Boolean value Yes/No N
-snucleotide3
-snucleotide_bsequence
boolean Sequence is nucleotide Boolean value Yes/No N
-sprotein3
-sprotein_bsequence
boolean Sequence is protein Boolean value Yes/No N
-slower3
-slower_bsequence
boolean Make lower case Boolean value Yes/No N
-supper3
-supper_bsequence
boolean Make upper case Boolean value Yes/No N
-sformat3
-sformat_bsequence
string Input sequence format Any string  
-sdbname3
-sdbname_bsequence
string Database name Any string  
-sid3
-sid_bsequence
string Entryname Any string  
-ufo3
-ufo_bsequence
string UFO features Any string  
-fformat3
-fformat_bsequence
string Features format Any string  
-fopenfile3
-fopenfile_bsequence
string Features file name Any string  
"-outfile" associated outfile qualifiers
-odirectory5
-odirectory_outfile
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

vrnaevalpair reads any normal sequence USAs.

Input files for usage example

File: cofold-red.fasta

>red
AUGAAGAUGA

File: cofold-red.con

....((((..

File: cofold-blue.fasta

>blue
CUGUCUGUCUUGAGACA

File: cofold-blue.con

..))))(((....))).

Output file format

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

Output files for usage example

File: red.vrnaevalpair

AUGAAGAUGA&CUGUCUGUCUUGAGACA
....((((..&..))))(((....))). ( -3.30)

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 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
vrnacofoldpf RNA cofolding with partitioning
vrnadistance RNA distances
vrnaduplex RNA duplex calculation
vrnaeval RNA eval
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.

Please report all bugs to the EMBOSS bug team (emboss-bug © 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.

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