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vrnaduplex |
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% vrnaduplex RNA duplex calculation Input nucleotide sequence: cofold-red.fasta Second nucleotide sequence: cofold-blue.fasta Vienna RNAfold output file [red.vrnaduplex]: |
Go to the input files for this example
Go to the output files for this example
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 [*.vrnaduplex] 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 is accepted)
-[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. 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 | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| [-asequence] (Parameter 1) |
Nucleotide sequence filename and optional format, or reference (input USA) | Readable sequence | Required | ||||||||
| [-bsequence] (Parameter 2) |
Nucleotide sequence filename and optional format, or reference (input USA) | Readable sequence | Required | ||||||||
| [-outfile] (Parameter 3) |
Vienna RNAfold output file | Output file | <*>.vrnaduplex | ||||||||
| Additional (Optional) qualifiers | Allowed values | Default | |||||||||
| (none) | |||||||||||
| Advanced (Unprompted) qualifiers | Allowed values | Default | |||||||||
| -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 | ||||||||
| -delta | Energy range for suboptimal structures | Any numeric value | -1.0 | ||||||||
| -sort | Sort suboptimal structures | Boolean value Yes/No | No | ||||||||
| -dangles | Method |
|
1 | ||||||||
>red AUGAAGAUGA |
>blue CUGUCUGUCUUGAGACA |
.(.(((((.&.))))).). 1,9 : 6,14 (-4.10) |
| 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 |
| 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 |
| vrnalfold | Calculate locally stable secondary structures of RNAs |
| vrnaplot | Plot vrnafold output |
| vrnasubopt | Calculate RNA suboptimals |
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.