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vrnaevalpair |
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The original program has additional inputs and produces different outputs, depending on the options selected. In the EMBASSY implementation it is split into vrnaeval and vrnaevalpair
% vrnaevalpair RNA eval with cofold Input nucleotide sequence: cofold-red.fasta Vienna RNA structure constraints file: cofold-red.con Second nucleotide sequence: cofold-blue.fasta Second vienna RNA structure constraints file: cofold-blue.con Vienna RNAeval output file [red.vrnaevalpair]: |
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)
[-aconstraintfile] infile Vienna RNA structure constraints file
[-bsequence] sequence Nucleotide sequence filename and optional
format, or reference (input USA)
[-bconstraintfile] infile Second vienna RNA structure constraints file
[-outfile] outfile [*.vrnaevalpair] Vienna RNAeval 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]convert boolean [Y] Convert T to U
-[no]tetraloop boolean [Y] Stabilising energies for tetra-loops
-circular boolean [N] Circular RNA
-energy menu [0] Rarely used option to fold sequences
from the ABCD... alphabet (Values: 0 (BP); 1
(Any with GC); 2 (Any with AU parameters))
-dangles menu [1] Method (Values: 0 (No stabilising
energies for dangling ends); 1 (Use
stabilising energies for dangling ends); 2
(Dangling energies as in a partition
function 3:Allow coaxial stacking of
adjacent helices))
-logml boolean [N] Use log scale for multiloop energies
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
-sbegin3 integer Start of the sequence to be used
-send3 integer End of the sequence to be used
-sreverse3 boolean Reverse (if DNA)
-sask3 boolean Ask for begin/end/reverse
-snucleotide3 boolean Sequence is nucleotide
-sprotein3 boolean Sequence is protein
-slower3 boolean Make lower case
-supper3 boolean Make upper case
-sformat3 string Input sequence format
-sdbname3 string Database name
-sid3 string Entryname
-ufo3 string UFO features
-fformat3 string Features format
-fopenfile3 string Features file name
"-outfile" associated qualifiers
-odirectory5 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 | ||||||
| [-aconstraintfile] (Parameter 2) |
Vienna RNA structure constraints file | Input file | Required | ||||||
| [-bsequence] (Parameter 3) |
Nucleotide sequence filename and optional format, or reference (input USA) | Readable sequence | Required | ||||||
| [-bconstraintfile] (Parameter 4) |
Second vienna RNA structure constraints file | Input file | Required | ||||||
| [-outfile] (Parameter 5) |
Vienna RNAeval output file | Output file | <*>.vrnaevalpair | ||||||
| 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]convert | Convert T to U | Boolean value Yes/No | Yes | ||||||
| -[no]tetraloop | Stabilising energies for tetra-loops | Boolean value Yes/No | Yes | ||||||
| -circular | Circular RNA | Boolean value Yes/No | No | ||||||
| -energy | Rarely used option to fold sequences from the ABCD... alphabet |
|
0 | ||||||
| -dangles | Method |
|
1 | ||||||
| -logml | Use log scale for multiloop energies | Boolean value Yes/No | No | ||||||
>red AUGAAGAUGA |
....((((.. |
>blue CUGUCUGUCUUGAGACA |
..))))(((....))). |
AUGAAGAUGA&CUGUCUGUCUUGAGACA ....((((..&..))))(((....))). ( -4.40) |
| 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 |
| vrnaduplex | RNA duplex calculation |
| vrnaeval | RNA eval |
| 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.