                                ovrnainverse



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Function

   Find RNA sequences with a given secondary structure

Description

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

   It searches for sequences folding into a predefined structure, thereby
   inverting the folding algorithm. Target structures (in bracket
   notation) and starting sequences for the search are read.

Algorithm

   Characters in the start sequence other than "AUGC" (or the alphabet
   specified with -a) are treated as wild cards and replaced by a random
   character. Any lower case characters in the start sequence are kept
   fixed during the search. If necessary, the sequence will be elongated
   to the length of the structure. Thus a string of "N"s as well as a
   blank line specify a random start sequence.

   For each search the best sequence found and its Hamming distance to the
   start sequence are output. If the the search was unsuccessful, a
   structure distance to the target is appended. Optionally the output
   format can be modified.

   The program will continue to read new structures and sequences until a
   line consisting of the single character "@" or an end of file condition
   is encountered.

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

Usage

   Here is a sample session with ovrnainverse


% ovrnainverse -repeats 3
Find RNA sequences with a given secondary structure
Vienna RNA structures file: rna3.fold
Vienna RNAfold output file [rna3.ovrnainverse]:


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

   Example 2


% ovrnainverse -repeats 3 -succeed
Find RNA sequences with a given secondary structure
Vienna RNA structures file: rna3.fold
Vienna RNAfold output file [rna3.ovrnainverse]:


   Go to the output files for this example

Command line arguments

Find RNA sequences with a given secondary structure
Version: EMBOSS:6.6.0.0

   Standard (Mandatory) qualifiers:
  [-structuresfile]    infile     Vienna RNA structures file
  [-outfile]           outfile    [*.ovrnainverse] 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)
   -[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)
   -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
   -scircular          boolean    Sequence is circular
   -squick             boolean    Read id and sequence only
   -sformat            string     Input sequence format
   -iquery             string     Input query fields or ID list
   -ioffset            integer    Input start position offset
   -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 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


Input file format

   ovrnainverse reads any normal sequence USAs.

  Input files for usage example

  File: rna3.fold

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

Output file format

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

  Output files for usage example

  File: rna3.ovrnainverse

CGGGUGUCCGGGCUGAUGCGUGCUCCGCCGUAACCGGGACGGCAAGUUUAGUCCUACAUCGACUAACACUCGACCG   3
2
CUAUGAUGAUGUAAACGAUACUACACUGGGCCGCUUCCGUCCACAUUGCGACCUUGCAUUGGUUGAUCGUGGUUAC   3
0
GUUCGGAAUCGAGCAUAUACACUCGUUAGCCAUUGAGCGGCUGCAACCGUGCACUUUUCCUGUACUCCGGACCGAA   1
5

  Output files for usage example 2

  File: rna3.ovrnainverse

UUAAACCACGUGUAGUAGGAAGCGCAUCAUUAUGAACAGAUGAGGGUAAGAACGGGGUGAGUUUUGGUUUAGAAAU   2
6
CUUUCAACGCUUGAUCCUUCCCAAGACACCAAAUCUCGUGGUGGCUGCGUCGGUUUCCCUUCGAUUUGAGAGUGAA   3
3
UUUACGGUCAGACACGGAUUAGUCUAAGCCGAUCUCCGCGGUUAACAACGGCCUAAACCUGGUCGCCGUAGAAACA   1
7

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
   banana           Plot bending and curvature data for B-DNA
   btwisted         Calculate the twisting in a B-DNA sequence
   einverted        Find inverted repeats in nucleotide sequences
   ovrnaalifold     Calculate secondary structures for a set of aligned RNAs
   ovrnaalifoldpf   Calculate secondary structures for a set of aligned RNAs
                    (partition)
   ovrnacofold      Calculate secondary structures of RNA dimers
   ovrnacofoldconc  Calculate secondary structures of RNA dimers
                    (concentrations)
   ovrnacofoldpf    Calculate secondary structures of RNA dimers
                    (partitioning)
   ovrnadistance    Calculate distances between RNA secondary structures
   ovrnaduplex      Predict RNA duplex (hybridization) sites and structure
   ovrnaeval        Calculate energy of RNA sequences with a given secondary
                    structure
   ovrnaevalpair    Calculate energy of RNA sequences on given secondary
                    structure
   ovrnafold        Calculate min. energy RNA structure / pair probabilities
                    (partition)
   ovrnafoldpf      Calculate min. energy RNA structure / pair probabilities
   ovrnaheat        Calculate specific heat of RNA melting
   ovrnalfold       Calculate locally stable secondary structures of RNAs
   ovrnaplot        Draw RNA secondary structures
   ovrnasubopt      Calculate suboptimal secondary structure of RNA
   sirna            Find siRNA duplexes in mRNA
   vrna2dfold       Calculate RNA structures and samples of k,l neighbourhoods
   vrnaaliduplex    RNA duplex calculation for two sequence alignments
   vrnaalifold      Calculate secondary structures for a set of aligned RNAs
   vrnaalifoldpf    Calculate secondary structures for a set of aligned RNAs
                    (partition)
   vrnacofold       Calculate secondary structures of RNA dimers
   vrnacofoldconc   Calculate secondary structures of RNA dimers
                    (concentrations)
   vrnacofoldpf     Calculate secondary structures of RNA dimers
                    (partitioning)
   vrnadistance     Calculate distances between RNA secondary structures
   vrnaduplex       Predict RNA duplex (hybridization) sites and structure
   vrnaeval         Calculate energy of RNA sequences with a given secondary
                    structure
   vrnaevalpair     Calculate energy of RNA sequences on given secondary
                    structure
   vrnafold         Calculate min. energy RNA secondary structures and pair
                    probabilities
   vrnafoldpf       Calculate min. energy RNA structures / pair probabilities
                    (partition)
   vrnaheat         Calculate specific heat of RNA melting
   vrnainverse      Find RNA sequences with a given secondary structure
   vrnalalifoldpf   Calculate secondary structures for a set of aligned RNAs
                    (partition)
   vrnalfold        Calculate locally stable secondary structures of RNAs
   vrnalfoldz       Calculate locally stable secondary structures of RNAs plus
                    zscore
   vrnapkplex       Calculate RNA structures plus pseudoknots
   vrnaplfold       Compute avg. pair probabilities for local base pairs in RNA
                    sequences
   vrnaplot         Draw RNA secondary structures
   vrnasubopt       Calculate suboptimal secondary structures of RNAs

Author(s)

   This program is an EMBOSS conversion of a program written by Ivo
   Hofacker as part of his VIENNA package.

   Please report all bugs to the EMBOSS bug team
   (emboss-bug (c) emboss.open-bio.org) 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
