vrna2dfold

 

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Function

Structures and samples of k,l neighbourhoods

Description

Computes MFE structure, partition function and representative sample structures of k,l neighborhoods.

Algorithm

Exploits sparse matrices aallows parallel computation of diagonal elements using OpenMP (if installed). Uses MFE computation, partition function computation and bolzmann sampling.

Uses the Turner 2004 nearest neighbor model.

Usage

Here is a sample session with vrna2dfold


% vrna2dfold 
Structures and samples of k,l neighbourhoods
Input nucleotide sequence: rnaaln1.seq
File of two dot-notation representative structures: rna2d.fold
Vienna RNAfold output file [rna1.vrna2dfold]: 

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

Command line arguments

Structures and samples of k,l neighbourhoods
Version: EMBOSS:6.4.0.0

   Standard (Mandatory) qualifiers:
  [-sequence]          sequence   Nucleotide sequence filename and optional
                                  format, or reference (input USA)
  [-constraintfile]    infile     File of two dot-notation representative
                                  structures
  [-outfile]           outfile    [*.vrna2dfold] Vienna RNAfold output file

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers:
   -paramfile          infile     Vienna RNA parameters file (optional)
   -partfunc           boolean    [N] Calculate partition function and
                                  Bolzmann probabilities
   -nback              integer    [0] Number of stochastic backtraces to
                                  display (Integer 0 or more)
   -neighbourhood      string     This can be specified multiple times
                                  (:,:,... (Any string)
   -scale              float      [1.07] Estimate of ensemble free energy (Any
                                  numeric value)
   -circular           boolean    [N] Circular RNA
   -temperature        float      [37.0] Temperature (Any numeric value)
   -onedist            integer    [-1] Maximum distance to first reference
                                  structure (Any integer value)
   -twodist            integer    [-1] Maximum distance to second reference
                                  structure (Any integer value)
   -[no]tetraloop      boolean    [Y] Stabilizing energies for tetra-loops
   -dangles            menu       [2] 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))
   -[no]gu             boolean    [Y] Allow GU pairs
   -[no]closegu        boolean    [Y] Allow GU pairs at end of helices
   -[no]convert        boolean    [Y] Convert T to U
   -nthreads           integer    [1] Number of threads (if OpenMP enabled in
                                  compilation) (Integer 1 or more)

   Associated qualifiers:

   "-sequence" associated qualifiers
   -sbegin1            integer    Start of the sequence to be used
   -send1              integer    End of the sequence to be used
   -sreverse1          boolean    Reverse (if DNA)
   -sask1              boolean    Ask for begin/end/reverse
   -snucleotide1       boolean    Sequence is nucleotide
   -sprotein1          boolean    Sequence is protein
   -slower1            boolean    Make lower case
   -supper1            boolean    Make upper case
   -sformat1           string     Input sequence format
   -sdbname1           string     Database name
   -sid1               string     Entryname
   -ufo1               string     UFO features
   -fformat1           string     Features format
   -fopenfile1         string     Features file name

   "-outfile" associated qualifiers
   -odirectory3        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

Qualifier Type Description Allowed values Default
Standard (Mandatory) qualifiers
[-sequence]
(Parameter 1)
sequence Nucleotide sequence filename and optional format, or reference (input USA) Readable sequence Required
[-constraintfile]
(Parameter 2)
infile File of two dot-notation representative structures Input file Required
[-outfile]
(Parameter 3)
outfile Vienna RNAfold output file Output file <*>.vrna2dfold
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
-paramfile infile Vienna RNA parameters file (optional) Input file Required
-partfunc boolean Calculate partition function and Bolzmann probabilities Boolean value Yes/No No
-nback integer Number of stochastic backtraces to display Integer 0 or more 0
-neighbourhood string This can be specified multiple times (<k>:<l>,<m>:<n>,... Any string  
-scale float Estimate of ensemble free energy Any numeric value 1.07
-circular boolean Circular RNA Boolean value Yes/No No
-temperature float Temperature Any numeric value 37.0
-onedist integer Maximum distance to first reference structure Any integer value -1
-twodist integer Maximum distance to second reference structure Any integer value -1
-[no]tetraloop boolean Stabilizing energies for tetra-loops Boolean value Yes/No Yes
-dangles list Method
0 (Ignore)
1 (Only unpaired bases for just one dangling end)
2 (Always use dangling energies)
3 (Allow coaxial stacking of adjacent helices)
2
-[no]gu boolean Allow GU pairs Boolean value Yes/No Yes
-[no]closegu boolean Allow GU pairs at end of helices Boolean value Yes/No Yes
-[no]convert boolean Convert T to U Boolean value Yes/No Yes
-nthreads integer Number of threads (if OpenMP enabled in compilation) Integer 1 or more 1
Associated qualifiers
"-sequence" associated sequence qualifiers
-sbegin1
-sbegin_sequence
integer Start of the sequence to be used Any integer value 0
-send1
-send_sequence
integer End of the sequence to be used Any integer value 0
-sreverse1
-sreverse_sequence
boolean Reverse (if DNA) Boolean value Yes/No N
-sask1
-sask_sequence
boolean Ask for begin/end/reverse Boolean value Yes/No N
-snucleotide1
-snucleotide_sequence
boolean Sequence is nucleotide Boolean value Yes/No N
-sprotein1
-sprotein_sequence
boolean Sequence is protein Boolean value Yes/No N
-slower1
-slower_sequence
boolean Make lower case Boolean value Yes/No N
-supper1
-supper_sequence
boolean Make upper case Boolean value Yes/No N
-sformat1
-sformat_sequence
string Input sequence format Any string  
-sdbname1
-sdbname_sequence
string Database name Any string  
-sid1
-sid_sequence
string Entryname Any string  
-ufo1
-ufo_sequence
string UFO features Any string  
-fformat1
-fformat_sequence
string Features format Any string  
-fopenfile1
-fopenfile_sequence
string Features file name Any string  
"-outfile" associated outfile qualifiers
-odirectory3
-odirectory_outfile
string Output directory Any string  
General qualifiers
-auto boolean Turn off prompts Boolean value Yes/No N
-stdout boolean Write first file to standard output Boolean value Yes/No N
-filter boolean Read first file from standard input, write first file to standard output Boolean value Yes/No N
-options boolean Prompt for standard and additional values Boolean value Yes/No N
-debug boolean Write debug output to program.dbg Boolean value Yes/No N
-verbose boolean Report some/full command line options Boolean value Yes/No Y
-help boolean Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose Boolean value Yes/No N
-warning boolean Report warnings Boolean value Yes/No Y
-error boolean Report errors Boolean value Yes/No Y
-fatal boolean Report fatal errors Boolean value Yes/No Y
-die boolean Report dying program messages Boolean value Yes/No Y
-version boolean Report version number and exit Boolean value Yes/No N

Input file format

vrna2dfold reads any normal sequence USAs.

Input files for usage example

File: rnaaln1.seq

>rna1
CACUACUCCAAGGACCGUAUCUUUCUCAGUGCGACAGUAA
>rna2
---UACUCCAAGGACCGUAUCUUUCUCAGUGCGACAG---

File: rna2d.fold

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

Output file format

vrna2dfold outputs a graph to the specified graphics device. outputs a report format file. The default format is ...

Output files for usage example

File: rna1.vrna2dfold

CACUACUCCAAGGACCGUAUCUUUCUCAGUGCGACAGUAA
...............(((((........)))))....... ( -3.00)
...............(((((........)))))....... ( -3.00) <ref 1>
................((((........))))........ ( -0.70) <ref 2>
k	l	MFE	MFE-structure
0	1	 -3.00	...............(((((........))))).......
1	0	 -0.70	................((((........))))........
1	2	 -1.30	............(..(((((........))))).).....
2	1	  0.30	..............(.((((........))))).......
2	3	 -2.20	......((....)).(((((........))))).......
3	2	  0.10	......((....))..((((........))))........
3	4	 -1.80	...............((((.((.....)))))).......
4	3	  0.50	................(((.((.....)))))........
4	5	 -1.60	...((((........(((((........)))))..)))).
5	4	  0.00	........................................
5	6	 -1.40	...((((....(...(((((........))))).))))).
6	5	  0.90	...((((....(....((((........))))..))))).
6	7	 -0.20	(.((......)))..((((.((.....)))))).......
7	6	  0.70	..............................((....))..
7	8	 -0.40	...((((........((((.((.....))))))..)))).
8	7	 -0.80	.............................(((....))).
8	9	 -0.20	...((((....(...((((.((.....)))))).))))).
9	8	 -0.10	..........((((........))))..............
9	10	  1.40	...((((....(...(((..((.....)).))).))))).
10	9	 -0.60	.........(((((.....)))))................
10	11	  4.00	...((((....(...((...((.....))..)).))))).
11	10	 -0.70	((((......((........)).....)))).........
11	12	  6.20	...((((....(...(....((.....))...).))))).
12	11	 -1.80	((((.....(((........)))....)))).........
12	13	  9.40	...((((....(...(...(((.....)).).).))))).
13	12	 -1.70	((((.....((((......))))....)))).........
13	14	 14.00	.(((.((...))(..(...(((.....)).).).))))..
14	13	 -2.70	((((.....(((((.....)))))...)))).........
14	15	 24.10	.(((.((...))(..((...)(((...)).).).))))..
15	14	 -1.50	..(((((..(((((.....)))))...)))).).......
16	15	 -0.10	.((((((..(((((.....)))))...))).....)))..
17	16	  3.00	.(((..((((((((..(...).))))...)).)).)))..
18	17	 10.90	.(((..((((((((...).)))((...)))).)).)))..

Data files

None.

Notes

None.

References

Turner & Mathews (2009). Nucleic Acids Research. 38, D280-D282.

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 Finds inverted repeats in nucleotide sequences
ovrnaalifold RNA alignment folding
ovrnaalifoldpf RNA alignment folding with partition
ovrnacofold RNA cofolding
ovrnacofoldconc RNA cofolding with concentrations
ovrnacofoldpf RNA cofolding with partitioning
ovrnadistance RNA distances
ovrnaduplex RNA duplex calculation
ovrnaeval RNA eval
ovrnaevalpair RNA eval with cofold
ovrnafold Calculate secondary structures of RNAs
ovrnafoldpf Secondary structures of RNAs with partition
ovrnaheat RNA melting
ovrnainverse RNA sequences matching a structure
ovrnalfold Calculate locally stable secondary structures of RNAs
ovrnaplot Plot vrnafold output
ovrnasubopt Calculate RNA suboptimals
sirna Finds siRNA duplexes in mRNA
vrnaaliduplex RNA duplex calculation for two sequence alignments
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
vrnainverse RNA sequences matching a structure
vrnalalifoldpf Locally stable 2ry structures for a set of aligned RNAs
vrnalfold Calculate locally stable secondary structures of RNAs
vrnalfoldz Locally stable secondary structures of RNAs plus zscore
vrnapkplex RNA structures plus pseudoknots
vrnaplfold Locally stable RNA 2ry structures - pair probabilities
vrnaplot Plot vrnafold output
vrnasubopt Calculate RNA suboptimals

Author(s)

Alan Bleasby
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK

Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.

History

Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.

Comments

None