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vrnaalifoldpf |
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The original program produces different outputs, depending on the options selected. In the EMBASSY implementation it is split into vrnaalifold and vrnaalifoldpf
% vrnaalifoldpf RNA alignment folding with partition Input (aligned) nucleotide sequence set: ecoli6s.fasta Vienna RNAfold output file [ecoli6s.vrnaalifoldpf]: |
Go to the input files for this example
Go to the output files for this example
RNA alignment folding with partition
Version: EMBOSS:6.3.0
Standard (Mandatory) qualifiers:
[-sequence] seqset (Aligned) nucleotide sequence set filename
and optional format, or reference (input
USA)
[-outfile] outfile [*.vrnaalifoldpf] 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)
-[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
-circular boolean [N] Circular RNA
-colour boolean [N] Colour structure plot
-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))
-scale float [1.07] Estimate of ensemble free energy (Any
numeric value)
-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))
-covariance float [1.0] Weight for covariance (Any numeric
value)
-nspenalty float [1.0] Non-compatible sequence penalty (Any
numeric value)
-endgaps boolean [N] Mark end gaps
-most boolean [N] Use most informative sequence algorithm
-dotoutfile outfile [*.vrnaalifoldpf] Vienna dotplot postscript
output file (optional)
-ssoutfile outfile [*.vrnaalifoldpf] Vienna RNA structure
postscript output file
-alignoutfile outfile [*.vrnaalifoldpf] Vienna RNA alignment
postscript output file (optional)
Associated qualifiers:
"-sequence" associated qualifiers
-sbegin1 integer Start of each sequence to be used
-send1 integer End of each 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
"-dotoutfile" associated qualifiers
-odirectory string Output directory
"-ssoutfile" associated qualifiers
-odirectory string Output directory
"-alignoutfile" associated qualifiers
-odirectory 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) |
seqset | (Aligned) nucleotide sequence set filename and optional format, or reference (input USA) | Readable set of sequences | Required | ||||||||
| [-outfile] (Parameter 2) |
outfile | Vienna RNAfold output file | Output file | <*>.vrnaalifoldpf | ||||||||
| 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 | ||||||||
| -[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 | ||||||||
| -circular | boolean | Circular RNA | Boolean value Yes/No | No | ||||||||
| -colour | boolean | Colour structure plot | Boolean value Yes/No | No | ||||||||
| -energy | list | Rarely used option to fold sequences from the ABCD... alphabet |
|
0 | ||||||||
| -scale | float | Estimate of ensemble free energy | Any numeric value | 1.07 | ||||||||
| -dangles | list | Method |
|
2 | ||||||||
| -covariance | float | Weight for covariance | Any numeric value | 1.0 | ||||||||
| -nspenalty | float | Non-compatible sequence penalty | Any numeric value | 1.0 | ||||||||
| -endgaps | boolean | Mark end gaps | Boolean value Yes/No | No | ||||||||
| -most | boolean | Use most informative sequence algorithm | Boolean value Yes/No | No | ||||||||
| -dotoutfile | outfile | Vienna dotplot postscript output file (optional) | Output file | <*>.vrnaalifoldpf | ||||||||
| -ssoutfile | outfile | Vienna RNA structure postscript output file | Output file | <*>.vrnaalifoldpf | ||||||||
| -alignoutfile | outfile | Vienna RNA alignment postscript output file (optional) | Output file | <*>.vrnaalifoldpf | ||||||||
| Associated qualifiers | ||||||||||||
| "-sequence" associated seqset qualifiers | ||||||||||||
| -sbegin1 -sbegin_sequence |
integer | Start of each sequence to be used | Any integer value | 0 | ||||||||
| -send1 -send_sequence |
integer | End of each 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 | |||||||||
| "-dotoutfile" associated outfile qualifiers | ||||||||||||
| -odirectory | string | Output directory | Any string | |||||||||
| "-ssoutfile" associated outfile qualifiers | ||||||||||||
| -odirectory | string | Output directory | Any string | |||||||||
| "-alignoutfile" associated outfile qualifiers | ||||||||||||
| -odirectory | 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 | ||||||||
>X01238.1/1-183 AUUUCUCUGAGAUGUUCGCAAGCGGGC.CAGUCCCCUGAGCCGAUAUUUCAUACCACAAG AAUGUGGCGCUCCGCGGUUGGUGAGCAUGCUCGGUCCGU...............CCGAGA AGCCUUAAAACUGCGACGACACAUUCACCUUGAACCAA.GGGUUCAAGGGUUACAGCCUG CGGCGGCA.UC.UCGGAG.AUUC >AL627277.1/108623-108805 AUUUCUCUGAGAUGUUUGCAAGCGGGC.CAGUCCCCUGAGCCGAUAUUUCAUACCACAAG AAUGUGGCGCUCCGCGGUUGGUGAGCAUGCUCGGUUCGU...............CCGAGA AGCCUUAAAACUGUGACGACACAUUCACCUUGAACCAA.GGGUUCAAGGGUUACAGCCUG CGGCGGCA.UC.UCGGAG.AUUC >AJ414145.1/90993-91174 AUUUCUCUGAGGUGUUUGCCAGCGGGC.CAGUCCCCUGAGCCGAUAUUUAAUACCAACAG AAUGUAGUGCUCCGUAACCGGUGAGCAUGCUCGGUCCG................CCGAGA AGCCUUAAGGUUGCGACGCUGCGUUCACCUUGAACCAA.GGGUUCAAGGGUUACAGCCUG CGACGGCA.CC.UCGGAG.AUCC >U32767.1/6538-6734 .AUUACCUGGAGUGUUCGUCAGUAGGC.UAUGUCCCUGAGCCGAUACUUUAAAUCUUAUA AAUU.GGUUUCCUAUCGUUGGUGUGUAGGCUUAACCUUUGACUCGUUCAUUGGGCUAAGA AACCUGAAAACGGUAUCAACUGAUUU.CCUUGAACCGUCGGGUUCAAGGACUACUGCCCG CAGCGGCACUC.UGGGGU.CUUC >AE006208.1/8365-8185 .AUUACCUGAGGUGUUUGCCAGUGGGU.UAUGUCCCUGAGCCGAUACUUU.UAUUUUAUG AAUC.GGUUUCUAAUUGUUGGUGUGCAUGCUUAGCUUGA...............CUAAGA AGCCUAAAAAUAGUUAUAACUGAUUC.CCUUGAACCGUUGGGUUCAAGGACUGAGACUUG CAGCGGCA.UC.UCGGGUUCUUC >Y00334.1/77-254 CGCUCCCUGGUGUGUUGGCCAGUCGGU.GAUGUCCCUGAGCCGAUAACUGCAACAAC..G GAGGUUGC.CAGUUGGACCGGUGUGCAUGUCCGCACG.................ACGGAA AGCCUUAAGGUCUAC.UGCAACCGCCACCUUGAACUUUCGGGUUCAAGGGCUA.ACCCGA CAGCGGCA.CGACCGGGG.AGCU >AE004317.1/5626-5807 UUUACCCUGGGGUGUUCGUCAGCGGAUUUAUGUCCCUGAGCCGAUAAGCAACAUAAC..A GGGUUGGUAUUGGGUAGCUAUUGAGCAAGCUCGGCUUGUA..............CCGAGA AGCCUGCGGUUACCAUUACUGAUCCG.CCUUGAACCUGAUGGUUCAAGGGCUACGAUCCU CAACGGCA.UC.CCGGGG.UUC. |
![[vrnaalifoldpf results]](vrnaalifoldpf.1.ecoli6s.ss.gif)
![[vrnaalifoldpf results]](vrnaalifoldpf.1.ecoli6s.gif)
![[vrnaalifoldpf results]](vrnaalifoldpf.1.ecoli6s.alirna.gif)
AUUUCCCUGAGGUGUUCGCCAGCGGGC_CAUGUCCCUGAGCCGAUAUUUAAUACCACAAGAAUGUGGUGCUCCGUGGUUGGUGAGCAUGCUCGGCCCGU_______________CCGAGAAGCCUUAAAAUUGCGACGACACAUUCACCUUGAACCAA_GGGUUCAAGGGCUACAGCCUGCAGCGGCA_UC_UCGGGG_AUUC
....(((((((((((.(((..((((((................................(((((((......(((((((...(.((...(((((....................)))))..)))....)))))))....))))))).(((((((((....)))))))))......)))))).)))))).)).))))))..... (-56.91 = -48.71 + -8.20)
....(((((((((({{(((..((((((................................(((((((......(((((((...{.((...(((((....................)))))..)),....)))))))..,.))))))).(((((((((....)))))))))......)))))).)))))).)).))))))..... [-59.30]
frequency of mfe structure in ensemble 0.0206905
# Alignment section
7 sequences; length of alignment 203
alifold output
64 142 0 100.0% 0.000 CG:1 GC:4 UG:1 UA:1
63 143 0 99.9% 0.002 GC:1 GU:1 UG:1 UA:4
74 134 0 99.8% 0.005 GC:3 GU:1 AU:2 UA:1
77 131 0 100.0% 0.001 GC:3 GU:2 AU:2
10 193 0 99.8% 0.006 GC:2 GU:1 AU:4
76 132 1 99.9% 0.003 CG:1 GC:1 GU:2 AU:1 UA:1
79 129 0 99.3% 0.032 CG:2 UG:1 UA:4
66 140 0 98.3% 0.056 GC:4 GU:1 AU:1 UA:1
92 117 0 100.0% 0.000 CG:5 UA:2
91 118 0 100.0% 0.001 CG:1 UA:6
6 197 0 100.0% 0.001 CG:4 UA:3
90 119 0 99.9% 0.003 CG:6 UA:1
61 145 0 99.8% 0.005 GC:2 AU:5
93 116 0 99.8% 0.007 GC:5 AU:2
75 133 1 99.9% 0.003 CG:2 GU:1 UG:3
7 196 0 100.0% 0.000 CG:7
78 130 1 99.9% 0.010 CG:2 UA:4
8 195 0 99.8% 0.007 UG:7
62 144 1 99.7% 0.010 GC:1 AU:5
9 194 1 99.9% 0.003 GC:6
86 122 0 98.0% 0.083 CG:6 UA:1
65 141 2 99.1% 0.028 UG:2 UA:3
60 146 1 98.4% 0.050 GC:5 AU:1
152 165 0 98.0% 0.170 GC:7
155 162 0 98.0% 0.170 CG:7
85 123 0 97.9% 0.102 GC:7
153 164 0 97.9% 0.141 AU:7
154 163 0 97.9% 0.142 AU:7
151 166 0 97.5% 0.170 UA:7
5 198 0 96.3% 0.110 CG:5 AU:2
150 167 0 96.2% 0.158 UA:7
25 178 0 95.2% 0.329 GC:6 GU:1
26 177 0 95.1% 0.319 GC:6 AU:1
23 180 1 95.0% 0.199 CG:3 UG:2 UA:1
24 179 1 95.0% 0.320 CG:1 GC:1 GU:4
22 181 0 93.7% 0.311 GC:7
149 168 0 93.7% 0.404 CG:7
156 161 0 92.4% 0.322 CG:6 UG:1
27 176 1 91.6% 0.277 CG:4 UA:2
18 184 0 90.9% 0.490 GC:7
73 135 2 88.8% 0.331 CG:3 AU:1 UA:1
[Part of this file has been deleted for brevity]
25 36 0 0.6% 0.518 GC:7 +
24 37 1 0.6% 0.725 GU:5 AU:1 +
85 124 0 0.3% 0.462 GC:7 +
101 107 0 0.3% 0.080 AU:1 --:6 +
16 188 0 0.3% 0.831 UA:7 +
102 114 0 0.2% 0.070 CG:1 --:6 +
103 113 0 0.2% 0.070 UG:1 --:6 +
104 112 0 0.2% 0.052 CG:1 --:6 +
34 38 0 0.2% 0.894 CG:7 +
16 25 0 0.2% 0.927 UG:7 +
101 110 0 0.2% 0.061 AU:1 --:6 +
34 43 0 0.2% 0.658 CG:7 +
38 42 0 0.2% 0.938 GC:7 +
37 43 0 0.1% 0.727 UG:7 +
105 111 0 0.1% 0.030 GU:1 --:6 +
101 106 0 0.1% 0.063 AU:1 --:6 +
148 152 0 0.1% 0.237 CG:7 +
35 43 0 0.1% 0.641 CG:7 +
25 35 0 0.1% 0.629 GC:7 +
84 126 2 0.1% 0.039 UG:1 AU:3 UA:1 +
103 114 0 0.1% 0.071 UG:1 --:6 +
107 114 0 0.1% 0.072 UG:1 --:6 +
36 169 0 0.1% 0.882 CG:7 +
156 160 1 0.1% 0.158 CG:5 UG:1 +
104 113 0 0.1% 0.058 CG:1 --:6 +
15 188 0 0.1% 0.501 UA:7 +
35 40 0 0.1% 0.939 CG:7 +
155 160 1 0.5% 0.136 CG:6 +
26 35 1 0.5% 0.639 GC:6 +
81 126 2 0.2% 0.101 GU:4 UG:1 +
40 47 2 0.2% 0.584 GC:2 GU:3 +
81 123 1 0.4% 0.129 GC:6 +
80 124 1 0.4% 0.460 GC:6 +
151 157 2 0.2% 0.073 UG:2 UA:3 +
70 135 2 0.2% 0.499 CG:3 UA:2 +
82 127 1 0.3% 0.077 UA:6 +
81 125 1 0.3% 0.339 GU:6 +
19 182 2 0.1% 0.249 CG:3 UA:2 +
67 72 2 0.1% 0.036 GC:4 GU:1 +
79 128 2 0.1% 0.028 UG:1 UA:4 +
81 124 1 0.2% 0.483 GC:6 +
149 160 1 0.2% 0.141 CG:6 +
14 191 1 0.1% 0.284 GC:6 +
26 34 1 0.1% 0.634 GC:6 +
148 160 1 0.1% 0.241 CG:6 +
44 49 1 0.1% 0.062 AU:6 +
39 48 2 0.2% 0.416 AU:5 +
35 170 2 0.2% 1.006 CG:5 +
24 36 2 0.1% 0.486 GC:5 +
20 25 2 0.1% 0.419 CG:5 +
....(((((((((({{(((..((((((................................(((((((......(((((((...{.((...(((((....................)))))..)),....)))))))..,.))))))).(((((((((....)))))))))......)))))).)))))).)).)))))).....
|
| Program name | Description |
|---|---|
| einverted | Finds inverted repeats in nucleotide sequences |
| vrnaalifold | RNA alignment folding |
| 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 |
| vrnalfold | Calculate locally stable secondary structures of RNAs |
| 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.