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vrnacofoldconc |
The original program has additional inputs and produces different outputs, depending on the options selected. In the EMBASSY implementation it is split into vrnacofold vrnacofoldconc and vrnacofoldpf
% vrnacofoldconc RNA cofolding with concentrations Input nucleotide sequence: cofold-red.fasta Second nucleotide sequence: cofold-blue.fasta Vienna RNA concentration data file: cofold-conc.dat Vienna RNAfold output file [red.vrnacofoldconc]: |
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) [-concentrationfile] infile Vienna RNA concentration data file [-outfile] outfile [*.vrnacofoldconc] Vienna RNAfold output file Additional (Optional) qualifiers: (none) Advanced (Unprompted) qualifiers: -aconstraintfile infile Vienna RNA structure contraints file (optional) -bconstraintfile infile Second vienna RNA structure contraints 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 is accepted) -[no]tetraloop boolean [Y] Stabilizing energies for tetra-loops -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 [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)) -paired boolean [N] Calculate probabilities of base pairing -ssoutfile outfile [*.vrnacofoldconc] Output file name -aoutfile outfile [*.vrnacofoldconc] First (a) vienna dotplot output file -aaoutfile outfile [*.vrnacofoldconc] Second (a-a) vienna dotplot output file -boutfile outfile [*.vrnacofoldconc] Third (b) vienna dotplot output file -bboutfile outfile [*.vrnacofoldconc] Fourth (b-b) vienna dotplot output file -aboutfile outfile [*.vrnacofoldconc] Fifth (a-b) vienna dotplot output file 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 -odirectory4 string Output directory "-ssoutfile" associated qualifiers -odirectory string Output directory "-aoutfile" associated qualifiers -odirectory string Output directory "-aaoutfile" associated qualifiers -odirectory string Output directory "-boutfile" associated qualifiers -odirectory string Output directory "-bboutfile" associated qualifiers -odirectory string Output directory "-aboutfile" associated qualifiers -odirectory string Output directory General qualifiers: -auto boolean Turn off prompts -stdout boolean Write standard output -filter boolean Read standard input, write 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 | ||||||||
[-concentrationfile] (Parameter 3) |
Vienna RNA concentration data file | Input file | Required | ||||||||
[-outfile] (Parameter 4) |
Vienna RNAfold output file | Output file | <*>.vrnacofoldconc | ||||||||
Additional (Optional) qualifiers | Allowed values | Default | |||||||||
(none) | |||||||||||
Advanced (Unprompted) qualifiers | Allowed values | Default | |||||||||
-aconstraintfile | Vienna RNA structure contraints file (optional) | Input file | Required | ||||||||
-bconstraintfile | Second vienna RNA structure contraints file (optional) | Input file | Required | ||||||||
-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 | ||||||||
-energy | Rarely used option to fold sequences from the ABCD... alphabet |
|
0 | ||||||||
-scale | Estimate of ensemble free energy | Any numeric value | 1.07 | ||||||||
-dangles | Method |
|
1 | ||||||||
-paired | Calculate probabilities of base pairing | Boolean value Yes/No | No | ||||||||
-ssoutfile | Output file name | Output file | <*>.vrnacofoldconc | ||||||||
-aoutfile | First (a) vienna dotplot output file | Output file | <*>.vrnacofoldconc | ||||||||
-aaoutfile | Second (a-a) vienna dotplot output file | Output file | <*>.vrnacofoldconc | ||||||||
-boutfile | Third (b) vienna dotplot output file | Output file | <*>.vrnacofoldconc | ||||||||
-bboutfile | Fourth (b-b) vienna dotplot output file | Output file | <*>.vrnacofoldconc | ||||||||
-aboutfile | Fifth (a-b) vienna dotplot output file | Output file | <*>.vrnacofoldconc |
>red AUGAAGAUGA |
>blue CUGUCUGUCUUGAGACA |
10 10 |
AUGAAGAUGA&CUGUCUGUCUUGAGACA ....((((..&..))))(((....))). ( -4.40) Expinit2 = 0.513986 tab = -1.738299 taa = 4.679345 tbb = -12.558919 Free Energies: AB AA BB A B -5.884889 -0.208509 -16.658920 -0.003662 -4.266495 Initial concentrations Equilibrium concentrations A B AB AA BB A B 10.000000 10.000000 0.844630 3.676596 4.491062 1.802178 0.173246 f 10.000000 10.000000 0.042232 0.183830 0.224553 0.090109 0.008662 f ....((((,...)))}(((....))). [ -5.88] frequency of mfe structure in ensemble 0.279849 |
%!PS-Adobe-3.0 EPSF-3.0 %%Creator: ePS_dot.c,v 1.1 2005/10/13 13:00:44 ajb Exp $, ViennaRNA-1.6 %%CreationDate: Sat Jul 15 12:00:00 2006 %%Title: Rna secondary Structure Plot %%BoundingBox: 66 210 518 662 %%DocumentFonts: Helvetica %%Pages: 1 %%EndComments %Options: % to switch off outline pairs of sequence comment or % delete the appropriate line near the end of the file %%BeginProlog /RNAplot 100 dict def RNAplot begin /fsize 14 def /outlinecolor {0.2 setgray} bind def /paircolor {0.2 setgray} bind def /seqcolor {0 setgray} bind def /cshow { dup stringwidth pop -2 div fsize -3 div rmoveto show} bind def /min { 2 copy gt { exch } if pop } bind def /max { 2 copy lt { exch } if pop } bind def /drawoutline { outlinecolor newpath coor 0 get aload pop 0.8 0 360 arc coor {aload pop lineto} forall stroke } bind def /drawpairs { paircolor 0.7 setlinewidth [9 3.01] 9 setdash newpath pairs {aload pop coor exch 1 sub get aload pop moveto coor exch 1 sub get aload pop lineto } forall stroke } bind def % draw bases /drawbases { [] 0 setdash seqcolor 0 coor { aload pop moveto dup sequence exch 1 getinterval cshow 1 add [Part of this file has been deleted for brevity] AUGAAGAUGACUGUCUGUCUUGAGACA\ ) def /coor [ [96.276 111.415] [91.331 110.049] [86.992 106.486] [84.234 101.044] [83.858 94.465] [73.252 83.858] [62.645 73.252] [52.039 62.645] [36.067 58.926] [31.562 43.157] [43.157 31.562] [58.926 36.067] [62.645 52.039] [73.252 62.645] [83.858 73.252] [94.465 83.858] [107.979 90.367] [122.885 92.046] [137.791 93.726] [152.597 86.675] [165.951 96.194] [164.115 112.490] [148.978 118.799] [136.111 108.631] [121.206 106.952] [106.300 105.272] [104.357 108.419] ] def /pairs [ [5 16] [6 15] [7 14] [8 13] [17 26] [18 25] [19 24] ] def init % switch off outline pairs or bases by removing these lines drawoutline drawpairs drawbases % show it showpage end %%EOF |
%!PS-Adobe-3.0 EPSF-3.0 %%Title: RNA DotPlot %%Creator: ePS_dot.c,v 1.1 2005/10/13 13:00:44 ajb Exp $, ViennaRNA-1.6 %%CreationDate: Sat Jul 15 12:00:00 2006 %%BoundingBox: 66 211 518 662 %%DocumentFonts: Helvetica %%Pages: 1 %%EndComments %Options: -d2 % %FreeEnergy= -0.003661585 %This file contains the square roots of the base pair probabilities in the form % i j sqrt(p(i,j)) ubox %%BeginProlog /DPdict 100 dict def DPdict begin /logscale false def /box { %size x y box - draws box centered on x,y 2 index 0.5 mul add % x += 0.5 exch 2 index 0.5 mul add exch % x += 0.5 newpath moveto dup neg 0 rlineto dup neg 0 exch rlineto 0 rlineto closepath fill } bind def /ubox { logscale { log dup add lpmin div 1 exch sub dup 0 lt { pop 0 } if } if 3 1 roll exch len exch sub 1 add box } bind def /lbox { 3 1 roll len exch sub 1 add box } bind def /drawseq { % print sequence along all 4 sides [ [0.7 -0.3 0 ] [0.7 0.7 len add 0] [-0.3 len sub -0.4 -90] [Part of this file has been deleted for brevity] len lineto dup len exch sub 0 exch moveto len exch len exch sub lineto stroke } for [] 0 setdash 0.04 setlinewidth currentdict /cutpoint known { cutpoint 1 sub dup dup -1 moveto len 1 add lineto len exch sub dup -1 exch moveto len 1 add exch lineto stroke } if 0.5 neg dup translate } bind def end %%EndProlog DPdict begin %delete next line to get rid of title 270 665 moveto /Helvetica findfont 14 scalefont setfont (red.aps) show /sequence { (\ AUGAAGAUGA\ ) } def /len { sequence length } bind def 72 216 translate 72 6 mul len 1 add div dup scale /Helvetica findfont 0.95 scalefont setfont drawseq 0.5 dup translate % draw diagonal 0.04 setlinewidth 0 len moveto len 0 lineto stroke drawgrid %data starts here 1 8 0.056921184 ubox 2 6 0.010665222 ubox 2 7 0.059657315 ubox 2 9 0.037641368 ubox 2 10 0.014667470 ubox 3 8 0.016991073 ubox 4 8 0.013136244 ubox showpage end %%EOF |
%!PS-Adobe-3.0 EPSF-3.0 %%Title: RNA DotPlot %%Creator: ePS_dot.c,v 1.1 2005/10/13 13:00:44 ajb Exp $, ViennaRNA-1.6 %%CreationDate: Sat Jul 15 12:00:00 2006 %%BoundingBox: 66 211 518 662 %%DocumentFonts: Helvetica %%Pages: 1 %%EndComments %Options: -d2 % %FreeEnergy= -0.208508983 %This file contains the square roots of the base pair probabilities in the form % i j sqrt(p(i,j)) ubox %%BeginProlog /DPdict 100 dict def DPdict begin /logscale false def /box { %size x y box - draws box centered on x,y 2 index 0.5 mul add % x += 0.5 exch 2 index 0.5 mul add exch % x += 0.5 newpath moveto dup neg 0 rlineto dup neg 0 exch rlineto 0 rlineto closepath fill } bind def /ubox { logscale { log dup add lpmin div 1 exch sub dup 0 lt { pop 0 } if } if 3 1 roll exch len exch sub 1 add box } bind def /lbox { 3 1 roll len exch sub 1 add box } bind def /drawseq { % print sequence along all 4 sides [ [0.7 -0.3 0 ] [0.7 0.7 len add 0] [-0.3 len sub -0.4 -90] [Part of this file has been deleted for brevity] 0 len moveto len 0 lineto stroke drawgrid %data starts here 1 8 nan ubox 1 12 0.407831799 ubox 1 18 0.546335663 ubox 2 6 0.012910178 ubox 2 7 0.012773380 ubox 2 9 nan ubox 2 11 0.407831799 ubox 2 13 0.335096015 ubox 2 14 0.495435278 ubox 2 15 0.329519420 ubox 2 16 0.307465785 ubox 2 17 0.571406921 ubox 2 19 0.338549088 ubox 2 20 0.262470929 ubox 3 8 0.013692171 ubox 3 12 0.335096015 ubox 3 18 0.336299047 ubox 4 8 0.012403691 ubox 4 12 0.495435278 ubox 4 18 0.361298493 ubox 5 12 0.329519420 ubox 5 18 0.335687944 ubox 6 12 0.307465785 ubox 6 18 0.278217484 ubox 7 12 0.571406921 ubox 7 18 0.745965997 ubox 8 11 0.546335663 ubox 8 13 0.336299047 ubox 8 14 0.361298493 ubox 8 15 0.335687944 ubox 8 16 0.278217484 ubox 8 17 0.745965997 ubox 8 19 0.333927239 ubox 8 20 0.186733437 ubox 9 12 0.338549088 ubox 9 18 0.333927239 ubox 10 12 0.262470929 ubox 10 18 0.186733437 ubox 11 18 nan ubox 12 16 0.012910178 ubox 12 17 0.012773380 ubox 12 19 nan ubox 13 18 0.010583252 ubox 14 18 0.010427900 ubox showpage end %%EOF |
%!PS-Adobe-3.0 EPSF-3.0 %%Title: RNA DotPlot %%Creator: ePS_dot.c,v 1.1 2005/10/13 13:00:44 ajb Exp $, ViennaRNA-1.6 %%CreationDate: Sat Jul 15 12:00:00 2006 %%BoundingBox: 66 211 518 662 %%DocumentFonts: Helvetica %%Pages: 1 %%EndComments %Options: -d2 % %FreeEnergy= -5.884888649 %This file contains the square roots of the base pair probabilities in the form % i j sqrt(p(i,j)) ubox %%BeginProlog /DPdict 100 dict def DPdict begin /logscale false def /box { %size x y box - draws box centered on x,y 2 index 0.5 mul add % x += 0.5 exch 2 index 0.5 mul add exch % x += 0.5 newpath moveto dup neg 0 rlineto dup neg 0 exch rlineto 0 rlineto closepath fill } bind def /ubox { logscale { log dup add lpmin div 1 exch sub dup 0 lt { pop 0 } if } if 3 1 roll exch len exch sub 1 add box } bind def /lbox { 3 1 roll len exch sub 1 add box } bind def /drawseq { % print sequence along all 4 sides [ [0.7 -0.3 0 ] [0.7 0.7 len add 0] [-0.3 len sub -0.4 -90] [Part of this file has been deleted for brevity] 6 26 0.010568585 ubox 7 12 0.022464919 ubox 7 14 0.888581257 ubox 7 16 0.008014762 ubox 7 18 0.469788688 ubox 7 20 0.003434528 ubox 8 13 0.864846377 ubox 8 17 0.459064168 ubox 8 27 0.014069947 ubox 9 11 0.185631592 ubox 9 12 0.526055295 ubox 9 14 0.017371849 ubox 9 15 0.211168745 ubox 9 16 0.255225452 ubox 9 19 0.006477108 ubox 9 26 0.013490881 ubox 10 12 0.037689419 ubox 10 14 0.191228823 ubox 10 16 0.017643945 ubox 10 18 0.005857187 ubox 11 17 0.008887992 ubox 12 25 0.006033087 ubox 12 27 nan ubox 13 26 nan ubox 14 23 0.010075980 ubox 14 25 nan ubox 15 22 0.010247965 ubox 15 24 nan ubox 16 22 nan ubox 16 23 nan ubox 16 27 0.305588746 ubox 17 21 nan ubox 17 26 0.882047609 ubox 18 22 nan ubox 18 23 0.005436960 ubox 18 24 0.003329870 ubox 18 25 0.882815707 ubox 19 24 0.877600892 ubox 20 25 0.003423158 ubox 21 27 0.009348769 ubox 22 26 0.015430131 ubox 17 26 0.949999988 lbox 18 25 0.949999988 lbox 19 24 0.949999988 lbox 5 16 0.949999988 lbox 6 15 0.949999988 lbox 7 14 0.949999988 lbox 8 13 0.949999988 lbox showpage end %%EOF |
%!PS-Adobe-3.0 EPSF-3.0 %%Title: RNA DotPlot %%Creator: ePS_dot.c,v 1.1 2005/10/13 13:00:44 ajb Exp $, ViennaRNA-1.6 %%CreationDate: Sat Jul 15 12:00:00 2006 %%BoundingBox: 66 211 518 662 %%DocumentFonts: Helvetica %%Pages: 1 %%EndComments %Options: -d2 % %FreeEnergy= -4.266494751 %This file contains the square roots of the base pair probabilities in the form % i j sqrt(p(i,j)) ubox %%BeginProlog /DPdict 100 dict def DPdict begin /logscale false def /box { %size x y box - draws box centered on x,y 2 index 0.5 mul add % x += 0.5 exch 2 index 0.5 mul add exch % x += 0.5 newpath moveto dup neg 0 rlineto dup neg 0 exch rlineto 0 rlineto closepath fill } bind def /ubox { logscale { log dup add lpmin div 1 exch sub dup 0 lt { pop 0 } if } if 3 1 roll exch len exch sub 1 add box } bind def /lbox { 3 1 roll len exch sub 1 add box } bind def /drawseq { % print sequence along all 4 sides [ [0.7 -0.3 0 ] [0.7 0.7 len add 0] [-0.3 len sub -0.4 -90] [Part of this file has been deleted for brevity] } bind def end %%EndProlog DPdict begin %delete next line to get rid of title 270 665 moveto /Helvetica findfont 14 scalefont setfont (red.bps) show /sequence { (\ CUGUCUGUCUUGAGACA\ ) } def /len { sequence length } bind def 72 216 translate 72 6 mul len 1 add div dup scale /Helvetica findfont 0.95 scalefont setfont drawseq 0.5 dup translate % draw diagonal 0.04 setlinewidth 0 len moveto len 0 lineto stroke drawgrid %data starts here 1 14 0.005240367 ubox 2 13 0.004453976 ubox 2 15 0.020976246 ubox 2 17 0.670298457 ubox 3 9 0.003276457 ubox 3 16 0.947914389 ubox 4 13 0.030267916 ubox 4 15 0.948345709 ubox 5 12 0.031100569 ubox 5 14 0.948406578 ubox 6 12 0.036122707 ubox 6 13 0.895017467 ubox 6 17 0.221479258 ubox 7 11 0.028943407 ubox 7 16 0.313227070 ubox 8 12 0.034859252 ubox 8 13 0.014451769 ubox 8 15 0.313262201 ubox 9 14 0.311389763 ubox 3 16 0.949999988 lbox 4 15 0.949999988 lbox 5 14 0.949999988 lbox 6 13 0.949999988 lbox showpage end %%EOF |
%!PS-Adobe-3.0 EPSF-3.0 %%Title: RNA DotPlot %%Creator: ePS_dot.c,v 1.1 2005/10/13 13:00:44 ajb Exp $, ViennaRNA-1.6 %%CreationDate: Sat Jul 15 12:00:00 2006 %%BoundingBox: 66 211 518 662 %%DocumentFonts: Helvetica %%Pages: 1 %%EndComments %Options: -d2 % %FreeEnergy= -16.658920288 %This file contains the square roots of the base pair probabilities in the form % i j sqrt(p(i,j)) ubox %%BeginProlog /DPdict 100 dict def DPdict begin /logscale false def /box { %size x y box - draws box centered on x,y 2 index 0.5 mul add % x += 0.5 exch 2 index 0.5 mul add exch % x += 0.5 newpath moveto dup neg 0 rlineto dup neg 0 exch rlineto 0 rlineto closepath fill } bind def /ubox { logscale { log dup add lpmin div 1 exch sub dup 0 lt { pop 0 } if } if 3 1 roll exch len exch sub 1 add box } bind def /lbox { 3 1 roll len exch sub 1 add box } bind def /drawseq { % print sequence along all 4 sides [ [0.7 -0.3 0 ] [0.7 0.7 len add 0] [-0.3 len sub -0.4 -90] [Part of this file has been deleted for brevity] /cutpoint 18 def 72 216 translate 72 6 mul len 1 add div dup scale /Helvetica findfont 0.95 scalefont setfont drawseq 0.5 dup translate % draw diagonal 0.04 setlinewidth 0 len moveto len 0 lineto stroke drawgrid %data starts here 1 7 0.003236660 ubox 2 34 0.009973158 ubox 3 33 0.012492753 ubox 4 32 0.010908848 ubox 4 34 0.009627680 ubox 5 31 0.009623489 ubox 6 30 0.006572256 ubox 6 34 0.706536621 ubox 7 33 0.999220455 ubox 8 32 0.999725513 ubox 9 31 0.999931184 ubox 10 30 0.999844986 ubox 11 29 0.525401714 ubox 12 28 0.525401714 ubox 13 23 0.006572256 ubox 13 27 0.999844986 ubox 14 22 0.009623489 ubox 14 26 0.999931184 ubox 15 21 0.010908848 ubox 15 25 0.999725513 ubox 16 20 0.012492753 ubox 16 24 0.999220455 ubox 17 19 0.009973158 ubox 17 21 0.009627680 ubox 17 23 0.706536621 ubox 18 24 0.003236660 ubox 7 33 0.949999988 lbox 8 32 0.949999988 lbox 9 31 0.949999988 lbox 10 30 0.949999988 lbox 13 27 0.949999988 lbox 14 26 0.949999988 lbox 15 25 0.949999988 lbox 16 24 0.949999988 lbox showpage end %%EOF |
Program name | Description |
---|---|
einverted | Finds DNA inverted repeats |
vrnaalifold | RNA alignment folding |
vrnaalifoldpf | RNA alignment folding with partition |
vrnacofold | RNA cofolding |
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 |
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.