vrnainverse

 

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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

Standard (Mandatory) qualifiers Allowed values Default
[-structuresfile]
(Parameter 1)
Vienna RNA structures file Input file Required
[-outfile]
(Parameter 2)
Vienna RNAfold output file Output file <*>.vrnainverse
Additional (Optional) qualifiers Allowed values Default
(none)
Advanced (Unprompted) qualifiers Allowed values Default
-sequence Nucleotide sequence filename and optional format, or reference (input USA) Readable sequence Required
-paramfile Vienna RNA parameters file (optional) Input file Required
-temperature Temperature Any numeric value 37.0
-[no]gu Allow GU pairs Boolean value Yes/No Yes
-[no]closegu Allow GU pairs at end of helices Boolean value Yes/No Yes
-[no]lp Allow lonely pairs Boolean value Yes/No Yes
-[no]convert Convert T to U Boolean value Yes/No Yes
-nsbases Non-standard bases Any string is accepted An empty string is accepted
-[no]tetraloop Stabilizing energies for tetra-loops Boolean value Yes/No Yes
-energy Rarely used option to fold sequences from the ABCD... alphabet
0 (BP)
1 (Any with GC)
2 (Any with AU parameters)
0
-dangles Method
0 (Ignore)
1 (Only unpaired bases for just one dangling end)
2 (Always use dangling energies)
3 (Allow coaxial stacking of adjacent helices)
1
-folding Method
m (Minimum energy)
pv (Partition function)
mp (Both)
m
-alphabet Find sequences using only these bases Any string is accepted AUGC
-final Stopping value Any numeric value 0.0
-repeats Number of times to search for the same structure Integer 0 or more 0
-succeed The original RNAinverse uses a negative repeat for this Boolean value Yes/No No
-showfails Show information for unsuccessful searches Boolean value Yes/No No

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