vrnaevalpair

Wiki

Please help by correcting and extending the Wiki pages.

Function

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

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

Usage

% vrnaevalpair Calculate energy of RNA sequences on given secondary structure 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

Calculate energy of RNA sequences on given secondary structure
Version: EMBOSS:6.6.0.0

   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
   -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
   -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
   -scircular3         boolean    Sequence is circular
   -squick3            boolean    Read id and sequence only
   -sformat3           string     Input sequence format
   -iquery3            string     Input query fields or ID list
   -ioffset3           integer    Input start position offset
   -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
-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
-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
-scircular3 -scircular_bsequence	boolean	Sequence is circular	Boolean value Yes/No	N
-squick3 -squick_bsequence	boolean	Read id and sequence only	Boolean value Yes/No	N
-sformat3 -sformat_bsequence	string	Input sequence format	Any string
-iquery3 -iquery_bsequence	string	Input query fields or ID list	Any string
-ioffset3 -ioffset_bsequence	integer	Input start position offset	Any integer value	0
-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

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

Output files for usage example

File: red.vrnaevalpair

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

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