
                               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 contraints file: cofold-red.con
Second nucleotide sequence: cofold-blue.fasta
Second vienna RNA structure contraints 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 contraints file
  [-bsequence]         sequence   Nucleotide sequence filename and optional
                                  format, or reference (input USA)
  [-bconstraintfile]   infile     Second vienna RNA structure contraints 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
   -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 standard output
   -filter             boolean    Read standard input, write 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

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 DNA inverted repeats
   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
