                                ovrnadistance



Wiki

   The master copies of EMBOSS documentation are available at
   http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki.

   Please help by correcting and extending the Wiki pages.

Function

   Calculate distances between RNA secondary structures

Description

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

   It reads RNA secondary structures and calculates one or more measures
   for their dissimilarity, based on tree or string editing (alignment).
   In addition it calculates a "base pair distance" given by the number of
   base pairs present in one structure, but not the other. For structures
   of different length base pair distance is not recommended.

Algorithm

   RNAdistance accepts structures in bracket format, where matching
   brackets symbolize base pairs and unpaired bases are represented by a
   dot ".", or coarse grained representations where hairpins, interior
   loops, bulges, multiloops, stacks and external bases are represented by
   (H), (I), (B), (M), (S), and (E), respectively. These can be optionally
   weighted. Full structures can be represented in the same fashion using
   the identifiers (U) and (P) for unpaired and paired bases,
   respectively.

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

   The program will continue to read new structures until a line
   consisting of the single character @ or an end of file condition is
   encountered. Input lines neither containing a valid structure nor
   starting with > are ignored.

Usage

   Here is a sample session with ovrnadistance


% ovrnadistance -distance 'f,h' -doalignment
Calculate distances between RNA secondary structures
Vienna RNA structures file: rna4.fold
Vienna RNAfold output file [rna4.ovrnadistance]:


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

Command line arguments

Calculate distances between RNA secondary structures
Version: EMBOSS:6.6.0.0

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

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers:
   -distance           menu       [f] Distance types to calculate (Values: f
                                  (Full (tree)); h (HIT (tree)); w (Weighted
                                  coarse (tree)); c (Coarse (tree)); F (Full
                                  (string)); H (HIT (string)); W (Weighted
                                  coarse (string)); C (Coarse (string)); P
                                  (Base pair distance))
   -compare            menu       [p] Distance types to calculate (Values: p
                                  (Pairwise); m (Distance matrix between all
                                  structures); f (Compare all structures to
                                  the first one); c (Compare continuously))
   -schapiro           boolean    [N] Use cost matrix for comparing coarse
                                  structures
   -doalignment        boolean    [N] Alignment showing matching substructures

   Associated qualifiers:

   "-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

   ovrnadistance reads any normal sequence USAs.

  Input files for usage example

  File: rna4.fold

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

Output file format

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

  Output files for usage example

  File: rna4.ovrnadistance

f: 26
(_____(.(((__((((....._____))))_))).))....((..((((.....)))).)).
_.....(_(((..((((..........)))).)))_)_....__.__(((...._)))_.___
h: 32
(____((U1)((U5_)P7)(U1)P2)(U4)((U2)((U5)P4)(U1)P2)(U1)R1)
((U5)((U2)((U10)P4)(U1)P4)(U5)_____((U4)P3)(U1)_______R1)


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)
   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
   ovrnainverse     Find RNA sequences with a given secondary structure
   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
