ovrnasubopt |
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This is a port of the Vienna RNA package program RNAsubopt.
It reads RNA sequences and calculates all suboptimal secondary structures within a user-defined energy range above the minimum free energy (mfe). It prints the suboptimal structures in bracket notation followed by the energy in kcal/mol to stdout.
Optionally, it will produce Boltzmann weighted samples of secondary structures.
% ovrnasubopt Calculate RNA suboptimals Input nucleotide sequence: rna1.seq Vienna RNAfold output file [rna1.ovrnasubopt]: |
Go to the input files for this example
Go to the output files for this example
Calculate RNA suboptimals Version: EMBOSS:6.4.0.0 Standard (Mandatory) qualifiers: [-sequence] sequence Nucleotide sequence filename and optional format, or reference (input USA) [-outfile] outfile [*.ovrnasubopt] Vienna RNAfold output file Additional (Optional) qualifiers: (none) Advanced (Unprompted) qualifiers: -constraintfile infile Vienna RNA structure constraints file (optional) -paramfile infile Vienna RNA parameters file (optional) -temperature float [37.0] Temperature (Any numeric value) -circular boolean [N] Allow circular RNA -dos boolean [N] DOS special corrections -[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) -[no]tetraloop boolean [Y] Stabilizing energies for tetra-loops -erange float [1.0] Calculate suboptimal structures within erange of the mfe (Any numeric value) -prange float [0.0] Only print structures with energy within prange of the mfe (Any numeric value) -sort boolean [N] Sort structures by energy -logml boolean [N] Logarithmic energy function for multi-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)) -nrandom integer [0] Number of random suboptimal structures (Any integer value) 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 -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 |
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 | ||||||||
[-outfile] (Parameter 2) |
outfile | Vienna RNAfold output file | Output file | <*>.ovrnasubopt | ||||||||
Additional (Optional) qualifiers | ||||||||||||
(none) | ||||||||||||
Advanced (Unprompted) qualifiers | ||||||||||||
-constraintfile | infile | Vienna RNA structure constraints file (optional) | Input file | Required | ||||||||
-paramfile | infile | Vienna RNA parameters file (optional) | Input file | Required | ||||||||
-temperature | float | Temperature | Any numeric value | 37.0 | ||||||||
-circular | boolean | Allow circular RNA | Boolean value Yes/No | No | ||||||||
-dos | boolean | DOS special corrections | Boolean value Yes/No | No | ||||||||
-[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]lp | boolean | Allow lonely pairs | Boolean value Yes/No | Yes | ||||||||
-[no]convert | boolean | Convert T to U | Boolean value Yes/No | Yes | ||||||||
-nsbases | string | Non-standard bases | Any string | |||||||||
-[no]tetraloop | boolean | Stabilizing energies for tetra-loops | Boolean value Yes/No | Yes | ||||||||
-erange | float | Calculate suboptimal structures within erange of the mfe | Any numeric value | 1.0 | ||||||||
-prange | float | Only print structures with energy within prange of the mfe | Any numeric value | 0.0 | ||||||||
-sort | boolean | Sort structures by energy | Boolean value Yes/No | No | ||||||||
-logml | boolean | Logarithmic energy function for multi-loops | Boolean value Yes/No | No | ||||||||
-dangles | list | Method |
|
2 | ||||||||
-nrandom | integer | Number of random suboptimal structures | Any integer value | 0 | ||||||||
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 | ||||||||||||
-odirectory2 -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 |
> rna1 [100] CACUACUCCAAGGACCGUAUCUUUCUCAGUGCGACAGUAA -380 100 ...(((((....)).((((.((.....))))))...))). -2.80 ...(((((....)).(((((........)))))...))). -3.80 ...(((((....)..(((((........)))))..)))). -3.10 .(((..((....)).((((.((.....))))))..))).. -2.80 .(((..((....)).(((((........)))))..))).. -3.80 ......((....)).(((((........)))))....... -3.10 ...............(((((........)))))....... -3.30 |
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 |
sirna | Finds siRNA duplexes in mRNA |
vrna2dfold | Structures and samples of k,l neighbourhoods |
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 |
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.