
                               vrnadistance 



Function

   RNA distances

Description

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

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 vrnadistance


% vrnadistance -distance "f,h" -doalignment 
RNA distances
Vienna RNA structures file: rna4.fold
Vienna RNAfold output file [rna4.vrnadistance]: 

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

Command line arguments

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

   vrnadistance reads any normal sequence USAs.

  Input files for usage example

  File: rna4.fold

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

Output file format

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

  Output files for usage example

  File: rna4.vrnadistance

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
   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
   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
   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
