
                                vrnainverse 



Function

   RNA sequences matching a structure

Description

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

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 vrnainverse


% vrnainverse -repeats 3 
RNA sequences matching a structure
Vienna RNA structures file: rna3.fold
Vienna RNAfold output file [rna3.vrnainverse]: 

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

   Example 2


% vrnainverse -repeats 3 -succeed 
RNA sequences matching a structure
Vienna RNA structures file: rna3.fold
Vienna RNAfold output file [rna3.vrnainverse]: 

   Go to the output files for this example

Command line arguments

   Standard (Mandatory) qualifiers:
  [-structuresfile]    infile     Vienna RNA structures file
  [-outfile]           outfile    [*.vrnainverse] Vienna RNAfold output file

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers:
   -sequence           sequence   Nucleotide sequence filename and optional
                                  format, or reference (input USA)
   -paramfile          infile     Vienna RNA parameters file (optional)
   -temperature        float      [37.0] Temperature (Any numeric value)
   -[no]gu             boolean    [Y] Allow GU pairs
   -[no]closegu        boolean    [Y] Allow GU pairs at end of helices
   -[no]lp             boolean    [Y] Allow lonely pairs
   -[no]convert        boolean    [Y] Convert T to U
   -nsbases            string     Non-standard bases (Any string is accepted)
   -[no]tetraloop      boolean    [Y] Stabilizing 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 (Ignore); 1 (Only
                                  unpaired bases for just one dangling end); 2
                                  (Always use dangling energies); 3 (Allow
                                  coaxial stacking of adjacent helices))
   -folding            menu       [m] Method (Values: m (Minimum energy); pv
                                  (Partition function); mp (Both))
   -alphabet           string     [AUGC] Find sequences using only these bases
                                  (Any string is accepted)
   -final              float      [0.0] Stopping value (Any numeric value)
   -repeats            integer    [0] Number of times to search for the same
                                  structure (Integer 0 or more)
   -succeed            boolean    [N] The original RNAinverse uses a negative
                                  repeat for this
   -showfails          boolean    [N] Show information for unsuccessful
                                  searches

   Associated qualifiers:

   "-sequence" associated qualifiers
   -sbegin             integer    Start of the sequence to be used
   -send               integer    End of the sequence to be used
   -sreverse           boolean    Reverse (if DNA)
   -sask               boolean    Ask for begin/end/reverse
   -snucleotide        boolean    Sequence is nucleotide
   -sprotein           boolean    Sequence is protein
   -slower             boolean    Make lower case
   -supper             boolean    Make upper case
   -sformat            string     Input sequence format
   -sdbname            string     Database name
   -sid                string     Entryname
   -ufo                string     UFO features
   -fformat            string     Features format
   -fopenfile          string     Features file name

   "-outfile" associated qualifiers
   -odirectory2        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

Input file format

   vrnainverse reads any normal sequence USAs.

  Input files for usage example

  File: rna3.fold

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

Output file format

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

  Output files for usage example

  File: rna3.vrnainverse

AGCAUUAGAGCGGACUGAAAACUGCCCGGCUGUACUAAGGCCGUACCCCUGGUGUAUUGAACUAGUGAUGCUUUGU
26
GUGACUCACGAUCUGCGCAAUGGUCUAGCUGGAACUGAUAGCUUCUAAGAAUGAAUACGCCAUUCGGGUUAUCCCG
25
UGUAGUUACACCCCCGGAGUGGGGUUACGGGACGGAGUCUUGUUCGCAGUCGAUGUCACUUCGACGAUUACACCCG
34   d = 3.000000

  Output files for usage example 2

  File: rna3.vrnainverse

AGCAUUAGAGCGGACUGAAAACUGCCCGGCUGUACUAAGGCCGUACCCCUGGUGUAUUGAACUAGUGAUGCUUUGU
26
GUGACUCACGAUCUGCGCAAUGGUCUAGCUGGAACUGAUAGCUUCUAAGAAUGAAUACGCCAUUCGGGUUAUCCCG
25
GCUAUUAAACAGCUUAAGUCCGUUGCACUGCAAUAUUGGCAGUACCGCACCUAAUUCUAAUGGGUUAAUAGCAAUC
19

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
   vrnaevalpair   RNA eval with cofold
   vrnafold       Calculate secondary structures of RNAs
   vrnafoldpf     Secondary structures of RNAs with partition
   vrnaheat       RNA melting
   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
