vrna2dfold |
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Uses the Turner 2004 nearest neighbor model.
% 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]: |
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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 ( |
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 |
|
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 |
>rna1 CACUACUCCAAGGACCGUAUCUUUCUCAGUGCGACAGUAA >rna2 ---UACUCCAAGGACCGUAUCUUUCUCAGUGCGACAG--- |
...............(((((........)))))....... ................((((........))))........ |
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 .(((..((((((((...).)))((...)))).)).))).. |
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 |
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