ovrnaduplex |
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It reads two RNA sequences and computes optimal and suboptimal secondary structures for their hybridization. The calculation is simplified by allowing only inter-molecular base pairs, for the general case use ovrnacfold. The computed optimal and suboptimal structure are output. It is especially useful for computing the hybrid structure between a small probe sequence and a long target sequence.
% ovrnaduplex RNA duplex calculation Input nucleotide sequence: cofold-red.fasta Second nucleotide sequence: cofold-blue.fasta Vienna RNAfold output file [red.ovrnaduplex]: |
Go to the input files for this example
Go to the output files for this example
RNA duplex calculation Version: EMBOSS:6.4.0.0 Standard (Mandatory) qualifiers: [-asequence] sequence Nucleotide sequence filename and optional format, or reference (input USA) [-bsequence] sequence Nucleotide sequence filename and optional format, or reference (input USA) [-outfile] outfile [*.ovrnaduplex] Vienna RNAfold output file Additional (Optional) qualifiers: (none) Advanced (Unprompted) qualifiers: -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) -[no]tetraloop boolean [Y] Stabilizing energies for tetra-loops -delta float [-1.0] Energy range for suboptimal structures (Any numeric value) -sort boolean [N] Sort suboptimal structures -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)) Associated qualifiers: "-asequence" 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 "-bsequence" associated qualifiers -sbegin2 integer Start of the sequence to be used -send2 integer End of the sequence to be used -sreverse2 boolean Reverse (if DNA) -sask2 boolean Ask for begin/end/reverse -snucleotide2 boolean Sequence is nucleotide -sprotein2 boolean Sequence is protein -slower2 boolean Make lower case -supper2 boolean Make upper case -sformat2 string Input sequence format -sdbname2 string Database name -sid2 string Entryname -ufo2 string UFO features -fformat2 string Features format -fopenfile2 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 | ||||||||||||
[-asequence] (Parameter 1) |
sequence | Nucleotide sequence filename and optional format, or reference (input USA) | Readable sequence | Required | ||||||||
[-bsequence] (Parameter 2) |
sequence | Nucleotide sequence filename and optional format, or reference (input USA) | Readable sequence | Required | ||||||||
[-outfile] (Parameter 3) |
outfile | Vienna RNAfold output file | Output file | <*>.ovrnaduplex | ||||||||
Additional (Optional) qualifiers | ||||||||||||
(none) | ||||||||||||
Advanced (Unprompted) qualifiers | ||||||||||||
-paramfile | infile | Vienna RNA parameters file (optional) | Input file | Required | ||||||||
-temperature | float | Temperature | Any numeric value | 37.0 | ||||||||
-[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 | ||||||||
-delta | float | Energy range for suboptimal structures | Any numeric value | -1.0 | ||||||||
-sort | boolean | Sort suboptimal structures | Boolean value Yes/No | No | ||||||||
-dangles | list | Method |
|
1 | ||||||||
Associated qualifiers | ||||||||||||
"-asequence" associated sequence qualifiers | ||||||||||||
-sbegin1 -sbegin_asequence |
integer | Start of the sequence to be used | Any integer value | 0 | ||||||||
-send1 -send_asequence |
integer | End of the sequence to be used | Any integer value | 0 | ||||||||
-sreverse1 -sreverse_asequence |
boolean | Reverse (if DNA) | Boolean value Yes/No | N | ||||||||
-sask1 -sask_asequence |
boolean | Ask for begin/end/reverse | Boolean value Yes/No | N | ||||||||
-snucleotide1 -snucleotide_asequence |
boolean | Sequence is nucleotide | Boolean value Yes/No | N | ||||||||
-sprotein1 -sprotein_asequence |
boolean | Sequence is protein | Boolean value Yes/No | N | ||||||||
-slower1 -slower_asequence |
boolean | Make lower case | Boolean value Yes/No | N | ||||||||
-supper1 -supper_asequence |
boolean | Make upper case | Boolean value Yes/No | N | ||||||||
-sformat1 -sformat_asequence |
string | Input sequence format | Any string | |||||||||
-sdbname1 -sdbname_asequence |
string | Database name | Any string | |||||||||
-sid1 -sid_asequence |
string | Entryname | Any string | |||||||||
-ufo1 -ufo_asequence |
string | UFO features | Any string | |||||||||
-fformat1 -fformat_asequence |
string | Features format | Any string | |||||||||
-fopenfile1 -fopenfile_asequence |
string | Features file name | Any string | |||||||||
"-bsequence" associated sequence qualifiers | ||||||||||||
-sbegin2 -sbegin_bsequence |
integer | Start of the sequence to be used | Any integer value | 0 | ||||||||
-send2 -send_bsequence |
integer | End of the sequence to be used | Any integer value | 0 | ||||||||
-sreverse2 -sreverse_bsequence |
boolean | Reverse (if DNA) | Boolean value Yes/No | N | ||||||||
-sask2 -sask_bsequence |
boolean | Ask for begin/end/reverse | Boolean value Yes/No | N | ||||||||
-snucleotide2 -snucleotide_bsequence |
boolean | Sequence is nucleotide | Boolean value Yes/No | N | ||||||||
-sprotein2 -sprotein_bsequence |
boolean | Sequence is protein | Boolean value Yes/No | N | ||||||||
-slower2 -slower_bsequence |
boolean | Make lower case | Boolean value Yes/No | N | ||||||||
-supper2 -supper_bsequence |
boolean | Make upper case | Boolean value Yes/No | N | ||||||||
-sformat2 -sformat_bsequence |
string | Input sequence format | Any string | |||||||||
-sdbname2 -sdbname_bsequence |
string | Database name | Any string | |||||||||
-sid2 -sid_bsequence |
string | Entryname | Any string | |||||||||
-ufo2 -ufo_bsequence |
string | UFO features | Any string | |||||||||
-fformat2 -fformat_bsequence |
string | Features format | Any string | |||||||||
-fopenfile2 -fopenfile_bsequence |
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 |
>red AUGAAGAUGA |
>blue CUGUCUGUCUUGAGACA |
The computed optimal and suboptimal structure are outputwritten to stdout, one structure per line. Each line consist of: The structure in dot bracket format with a "&" separating the two strands. The range of the structure in the two sequences in the format "from,to : from,to"; the energy of duplex structure in kcal/mol.
.(.(((((.&.))))).). 1,9 : 6,14 (-4.10) |
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 |
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 |
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 |
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