vrnaevalpair

 

Function

RNA eval with cofold

Description

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

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

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

   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       [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:

   "-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. 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
[-aconstraintfile]
(Parameter 2)
Vienna RNA structure constraints file Input file Required
[-bsequence]
(Parameter 3)
Nucleotide sequence filename and optional format, or reference (input USA) Readable sequence Required
[-bconstraintfile]
(Parameter 4)
Second vienna RNA structure constraints file Input file Required
[-outfile]
(Parameter 5)
Vienna RNAeval output file Output file <*>.vrnaevalpair
Additional (Optional) qualifiers Allowed values Default
(none)
Advanced (Unprompted) qualifiers Allowed values Default
-paramfile Vienna RNA parameters file (optional) Input file Required
-temperature Temperature Any numeric value 37.0
-[no]convert Convert T to U Boolean value Yes/No Yes
-[no]tetraloop Stabilising energies for tetra-loops Boolean value Yes/No Yes
-circular Circular RNA Boolean value Yes/No No
-energy Rarely used option to fold sequences from the ABCD... alphabet
0 (BP)
1 (Any with GC)
2 (Any with AU parameters)
0
-dangles 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 Use log scale for multiloop energies Boolean value Yes/No No

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
....((((..&..))))(((....))). ( -4.40)

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
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
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