vrnaeval

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Function

Description

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

Usage

% vrnaeval RNA eval Input nucleotide sequence: evalrna.fasta Vienna RNA structure constraints file: eval1.con Vienna RNAeval output file [eval.vrnaeval]:

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

Command line arguments

RNA eval
Version: EMBOSS:6.3.0

   Standard (Mandatory) qualifiers:
  [-sequence]          sequence   Nucleotide sequence filename and optional
                                  format, or reference (input USA)
  [-constraintfile]    infile     Vienna RNA structure constraints file
  [-outfile]           outfile    [*.vrnaeval] 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       [1] 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:

   "-sequence" 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

   "-outfile" associated qualifiers
   -odirectory3        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
[-sequence] (Parameter 1)	sequence	Nucleotide sequence filename and optional format, or reference (input USA)	Readable sequence	Required
[-constraintfile] (Parameter 2)	infile	Vienna RNA structure constraints file	Input file	Required
[-outfile] (Parameter 3)	outfile	Vienna RNAeval output file	Output file	<*>.vrnaeval
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)	1
-logml	boolean	Use log scale for multiloop energies	Boolean value Yes/No	No
Associated qualifiers
"-sequence" associated sequence qualifiers
-sbegin1 -sbegin_sequence	integer	Start of the sequence to be used	Any integer value	0
-send1 -send_sequence	integer	End of the sequence to be used	Any integer value	0
-sreverse1 -sreverse_sequence	boolean	Reverse (if DNA)	Boolean value Yes/No	N
-sask1 -sask_sequence	boolean	Ask for begin/end/reverse	Boolean value Yes/No	N
-snucleotide1 -snucleotide_sequence	boolean	Sequence is nucleotide	Boolean value Yes/No	N
-sprotein1 -sprotein_sequence	boolean	Sequence is protein	Boolean value Yes/No	N
-slower1 -slower_sequence	boolean	Make lower case	Boolean value Yes/No	N
-supper1 -supper_sequence	boolean	Make upper case	Boolean value Yes/No	N
-sformat1 -sformat_sequence	string	Input sequence format	Any string
-sdbname1 -sdbname_sequence	string	Database name	Any string
-sid1 -sid_sequence	string	Entryname	Any string
-ufo1 -ufo_sequence	string	UFO features	Any string
-fformat1 -fformat_sequence	string	Features format	Any string
-fopenfile1 -fopenfile_sequence	string	Features file name	Any string
"-outfile" associated outfile qualifiers
-odirectory3 -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: evalrna.fasta

>eval
GGGGCCCCC

File: eval1.con

(...)....

Output file format

Output files for usage example

File: eval.vrnaeval

GGGGCCCCC
(...).... (  4.90)

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