vrnaplfold |
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Output consists of a dot plot in a postscript file, where the averaged pair probabilities can easily be parsed and visually inspected.
It is possible to compute the probability that a stretch of x consequtive nucleotides is unpaired, which is useful for predicting possible binding sites. Again this probability is averaged over all windows containing the region.
The output is a plain text matrix containing on each line a position i followed by the probability that i is unpaired, [i-1..i] is unpaired [i-2..i] is unpaired and so on to the probability that [i-x+1..i] is unpaired.
% vrnaplfold Locally stable RNA 2ry structures - pair probabilities Input nucleotide sequence: rna1.seq Vienna RNAfold output file [rna1.vrnaplfold]: |
Go to the input files for this example
Go to the output files for this example
Locally stable RNA 2ry structures - pair probabilities Version: EMBOSS:6.4.0.0 Standard (Mandatory) qualifiers: [-sequence] sequence Nucleotide sequence filename and optional format, or reference (input USA) [-outfile] outfile [*.vrnaplfold] Vienna RNAfold output file Additional (Optional) qualifiers: (none) Advanced (Unprompted) qualifiers: -paramfile infile Vienna RNA parameters file (optional) -winsize integer [70] Window size for averaging pair probabilities (Integer 2 or more) -separation integer [$(winsize)] Maximum allowed separation of a base pair to span (Any integer value) -cutoff float [0.01] Report only bp with avg prob > cutoff (Any numeric value) -onthefly boolean [N] Output during computation (automatic for very long seqs) -ulength integer [31] Calc mean probability that regions of ulength are unpaired (Integer 2 or more) -openenergy boolean [N] Output logarithms, not probabilities (activates ulength) -[no]convert boolean [Y] Convert T to U -temperature float [37.0] Temperature (Any numeric value) -[no]tetraloop boolean [Y] Stabilizing energies for tetra-loops -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)) -[no]lp boolean [Y] Allow lonely pairs -[no]gu boolean [Y] Allow GU pairs -[no]closegu boolean [Y] Allow GU pairs at end of helices -nsbases string Non-standard bases (Any string) -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)) -plexoutfile outfile [*.vrnaplfold] Vienna RNAplfold plex output file -ssoutfile outfile [*.vrnaplfold] Vienna RNA structure postscript output file Associated qualifiers: "-sequence" 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 "-outfile" associated qualifiers -odirectory2 string Output directory "-plexoutfile" associated qualifiers -odirectory string Output directory "-ssoutfile" 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) |
sequence | Nucleotide sequence filename and optional format, or reference (input USA) | Readable sequence | Required | ||||||||
[-outfile] (Parameter 2) |
outfile | Vienna RNAfold output file | Output file | <*>.vrnaplfold | ||||||||
Additional (Optional) qualifiers | ||||||||||||
(none) | ||||||||||||
Advanced (Unprompted) qualifiers | ||||||||||||
-paramfile | infile | Vienna RNA parameters file (optional) | Input file | Required | ||||||||
-winsize | integer | Window size for averaging pair probabilities | Integer 2 or more | 70 | ||||||||
-separation | integer | Maximum allowed separation of a base pair to span | Any integer value | $(winsize) | ||||||||
-cutoff | float | Report only bp with avg prob > cutoff | Any numeric value | 0.01 | ||||||||
-onthefly | boolean | Output during computation (automatic for very long seqs) | Boolean value Yes/No | No | ||||||||
-ulength | integer | Calc mean probability that regions of ulength are unpaired | Integer 2 or more | 31 | ||||||||
-openenergy | boolean | Output logarithms, not probabilities (activates ulength) | Boolean value Yes/No | No | ||||||||
-[no]convert | boolean | Convert T to U | Boolean value Yes/No | Yes | ||||||||
-temperature | float | Temperature | Any numeric value | 37.0 | ||||||||
-[no]tetraloop | boolean | Stabilizing energies for tetra-loops | Boolean value Yes/No | Yes | ||||||||
-dangles | list | Method |
|
2 | ||||||||
-[no]lp | boolean | Allow lonely pairs | Boolean value Yes/No | Yes | ||||||||
-[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 | ||||||||
-nsbases | string | Non-standard bases | Any string | |||||||||
-energy | list | Rarely used option to fold sequences from the ABCD... alphabet |
|
0 | ||||||||
-plexoutfile | outfile | Vienna RNAplfold plex output file | Output file | <*>.vrnaplfold | ||||||||
-ssoutfile | outfile | Vienna RNA structure postscript output file | Output file | <*>.vrnaplfold | ||||||||
Associated qualifiers | ||||||||||||
"-sequence" associated sequence qualifiers | ||||||||||||
-sbegin1 -sbegin_sequence |
integer | Start of the sequence to be used | Any integer value | 0 | ||||||||
-send1 -send_sequence |
integer | End of the 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 | |||||||||
"-plexoutfile" associated outfile qualifiers | ||||||||||||
-odirectory | string | Output directory | Any string | |||||||||
"-ssoutfile" 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 |
>rna1 CACUACUCCAAGGACCGUAUCUUUCUCAGUGCGACAGUAA |
#unpaired probabilities #i$ l=1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 1 0.7197006 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 2 0.7436407 0.6970294 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 3 0.6191163 0.6187358 0.6098213 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 4 0.498733 0.4495528 0.4492764 0.446118 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 5 0.7394522 0.448445 0.4234183 0.423145 0.4207406 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 6 0.6993007 0.6964077 0.4070592 0.383444 0.3832446 0.3809704 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 7 0.6459923 0.6230276 0.6203004 0.3416656 0.319917 0.319799 0.3175991 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 8 0.8914124 0.6331154 0.6131883 0.6104808 0.3325677 0.3109899 0.3108782 0.3086932 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 9 0.9779347 0.88718 0.6303147 0.6106271 0.6079246 0.3310934 0.3095998 0.3094893 0.3073068 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 10 0.6651365 0.66319 0.5726773 0.4026313 0.3905143 0.3899147 0.2912215 0.2843506 0.2843264 0.2822798 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 11 0.5181724 0.5024481 0.5009607 0.4144767 0.3013552 0.2914242 0.2912392 0.268241 0.2640238 0.2640165 0.2620029 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 12 0.3966587 0.3925504 0.3806482 0.3797934 0.2953032 0.2598187 0.2545819 0.254514 0.2499149 0.2490548 0.2490517 0.2482227 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 13 0.4166699 0.2701829 0.2672206 0.2664674 0.2661387 0.2657253 0.2402795 0.2374645 0.2374085 0.2339115 0.2335324 0.2335299 0.2335004 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 14 0.5077176 0.3548537 0.255988 0.2530381 0.2522964 0.2519891 0.2515976 0.2268277 0.2240578 0.2240024 0.2205592 0.2201829 0.2201804 0.2201509 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 15 0.9289085 0.5013714 0.3500168 0.2522725 0.2493285 0.2485947 0.2482889 0.2478983 0.2231985 0.2204339 0.220379 0.2169402 0.2165641 0.2165617 0.2165323 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 16 0.5491737 0.499974 0.1383552 0.06173901 0.01770257 0.01743567 0.01718166 0.01704812 0.01676035 0.0159869 0.01499615 0.01495264 0.01322167 0.01299422 0.01299253 0.01297731 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 17 0.492003 0.4915342 0.4789087 0.127728 0.05341019 0.01077281 0.01054951 0.0103734 0.01032887 0.01029984 0.009931776 0.009882992 0.009840096 0.008156462 0.007999311 0.007997643 0.007993475 NA NA NA NA NA NA NA NA NA NA NA NA NA NA 18 0.5300212 0.4908897 0.4904473 0.4778701 0.1273119 0.05311017 0.01052843 0.01032884 0.01015424 0.01010982 0.01008109 0.009714787 0.009666248 0.009625529 0.007942027 0.007784922 0.007783403 0.007779241 NA NA NA NA NA NA NA NA NA NA NA NA NA 19 0.5345269 0.5252989 0.4900584 0.4896358 0.4777258 0.1272482 0.0530616 0.01048893 0.0102895 0.0101175 0.01007345 0.01004503 0.009686363 0.009638501 0.00959781 0.007915753 0.007758765 0.007757246 0.007753087 NA NA NA NA NA NA NA NA NA NA NA NA 20 0.2938011 0.2178109 0.2093876 0.1741712 0.1737537 0.1618618 0.09264044 0.05281496 0.01031686 0.01021499 0.01004555 0.01000151 0.009973111 0.009617601 0.009570041 0.009529871 0.007848078 0.007691143 0.00768975 0.007685594 NA NA NA NA NA NA NA NA NA NA NA 21 0.5410661 0.1509547 0.1357306 0.1324175 0.09847581 0.09806244 0.08617698 0.01716552 0.01158671 0.009571132 0.009469874 0.00930615 0.009262353 0.009234453 0.00888206 0.008834842 0.00879475 0.007113214 0.006956324 0.006954971 0.006950825 NA NA NA NA NA NA NA NA NA NA 22 0.5486111 0.5381838 0.1494382 0.1345549 0.1313296 0.0976468 0.09723398 0.08535472 0.01659107 0.01137542 0.009478606 0.009428651 0.009282437 0.009238653 0.009210774 0.008859028 0.008811947 0.008772864 0.007091382 0.006934543 0.006933304 0.006929161 NA NA NA NA NA NA NA NA NA 23 0.5779542 0.4885846 0.4796176 0.09148143 0.07691182 0.0737204 0.041823 0.04141072 0.02953678 0.01647448 0.01128255 0.009417575 0.009397679 0.009258923 0.009215148 0.009187285 0.008835907 0.008788888 0.008751319 0.007069868 0.006913072 0.006911946 0.006907803 NA NA NA NA NA NA NA NA 24 0.6807958 0.564877 0.4782268 0.4700847 0.08214608 0.07005819 0.06688309 0.03556655 0.03515476 0.02328336 0.01419873 0.01118786 0.009335508 0.009321892 0.009187429 0.009143662 0.009115814 0.00876792 0.008721302 0.008686477 0.007005319 0.006848573 0.006847543 0.006843404 NA NA NA NA NA NA NA 25 0.9286778 0.6749446 0.5594603 0.4729211 0.4649512 0.07702016 0.06498695 0.06183046 0.03427249 0.03386097 0.02198973 0.01292678 0.01041049 0.009263179 0.009249608 0.009115283 0.00907155 0.009043804 0.008696801 0.008650266 0.008615445 0.006934362 0.006777625 0.006776596 0.00677246 NA NA NA NA NA NA 26 0.9226826 0.9135081 0.6621726 0.5495316 0.4634732 0.4555982 0.06768 0.05759898 0.05445764 0.027163 0.02675213 0.0148811 0.01265188 0.01026225 0.009130244 0.009119857 0.00898836 0.008944632 0.008916894 0.00857424 0.008528087 0.00852787 0.006847151 0.006690446 0.006689497 0.006685365 NA NA NA NA NA 27 0.9568866 0.8924959 0.8840739 0.6342872 0.521754 0.4357178 0.4278505 0.03993313 0.02986068 0.02672265 0.02627353 0.0258627 0.01399168 0.01176822 0.01020726 0.009110556 0.009100181 0.008968688 0.008924962 0.008897228 0.008554839 0.008508709 0.008508493 0.006827796 0.006671094 0.006670145 0.006666013 NA NA NA NA 28 0.5707227 0.5279095 0.5033991 0.4960224 0.4559324 0.4367568 0.4307586 0.4242831 0.03675038 0.02668882 0.02440408 0.02398079 0.02357612 0.0117051 0.009768442 0.008258639 0.007174381 0.007164079 0.007032592 0.006988866 0.006961132 0.006862964 0.006816834 0.006816618 0.00680398 0.006647277 0.006646329 0.006642197 NA NA NA 29 0.1000946 0.09936374 0.08651488 0.06806355 0.06403412 0.04164643 0.02935304 0.02491859 0.0238316 0.02373901 0.01413692 0.01187859 0.01146118 0.0114405 0.01142795 0.00953604 0.008035511 0.00695852 0.006948358 0.006816927 0.006779901 0.006755525 0.006659811 0.006643336 0.006643121 0.0066309 0.006620482 0.006619533 0.006618146 NA NA 30 0.04212957 0.02734344 0.02724145 0.02510973 0.02150803 0.01902369 0.01131287 0.007777365 0.006482667 0.005960174 0.005927005 0.005133633 0.003494208 0.00333512 0.003320714 0.003308208 0.002805891 0.002387648 0.001997445 0.001996324 0.00199592 0.001958894 0.00193452 0.001839876 0.001823508 0.001823441 0.001811239 0.001800831 0.001800826 0.00179944 NA 31 0.08970175 0.02378813 0.01796818 0.01793937 0.01638724 0.01394927 0.01212305 0.007262412 0.004782568 0.003863023 0.003622643 0.0035961 0.00299023 0.00272714 0.002589841 0.002583057 0.002575963 0.002190187 0.001866336 0.001535559 0.001534685 0.001534373 0.00152295 0.001500659 0.001406252 0.001393227 0.00139316 0.001380999 0.001379235 0.001379229 0.001378097 32 0.4046785 0.04197307 0.02227 0.01706292 0.01703848 0.01551884 0.0131867 0.01138409 0.006738941 0.004375689 0.00350003 0.003268632 0.003242948 0.002667915 0.002413869 0.002340781 0.002334089 0.002326994 0.001960578 0.001662951 0.001465021 0.001464188 0.001463892 0.001452469 0.001430178 0.001335786 0.001322762 0.001322697 0.001310536 0.001308771 0.001308766 33 0.4660732 0.3245468 0.03665849 0.01863054 0.01367627 0.01365318 0.01345239 0.01124228 0.01087654 0.006531392 0.004238782 0.003378075 0.003223865 0.003199462 0.002625391 0.002371841 0.002298849 0.002294138 0.00228949 0.00192369 0.001626166 0.001428299 0.001427467 0.00142717 0.001426869 0.001426658 0.001332375 0.001320984 0.001320919 0.001308773 0.001307655 34 0.9810539 0.4651036 0.3235795 0.03596802 0.01832148 0.01358025 0.01355982 0.01335927 0.01115417 0.01078872 0.006446877 0.004155445 0.003295065 0.003140877 0.003116621 0.002542614 0.002371484 0.002298501 0.00229379 0.002289142 0.00192339 0.001625902 0.001428056 0.001427224 0.001426927 0.001426626 0.001426414 0.001332204 0.001320813 0.001320748 0.001308625 35 0.9477427 0.929693 0.4635668 0.3229289 0.03585941 0.01821423 0.01356034 0.01354018 0.01333974 0.01113466 0.01076927 0.006427448 0.004136024 0.003275646 0.003121504 0.003097248 0.002523241 0.002352112 0.002283549 0.002278838 0.00227419 0.001908439 0.001612397 0.001428056 0.001427224 0.001426927 0.001426626 0.001426414 0.001332204 0.001320813 0.001320748 36 0.8765555 0.8529093 0.8443623 0.4130547 0.3142067 0.02942281 0.01663505 0.01250788 0.01248844 0.01237839 0.01045369 0.01011437 0.006139605 0.003972821 0.003156927 0.003005592 0.002981652 0.002407648 0.00223976 0.002172326 0.002167771 0.002163124 0.001798928 0.00150624 0.001322051 0.00132122 0.001320923 0.001320622 0.00132041 0.001320106 0.001308715 37 0.7453287 0.74477 0.7225333 0.7190154 0.3212035 0.311898 0.02909327 0.01644054 0.01234831 0.01232987 0.01225946 0.01035532 0.01002735 0.00608749 0.003931429 0.003118355 0.002969118 0.002953285 0.00238114 0.002213445 0.002146069 0.00214438 0.00214438 0.001785406 0.001492861 0.001308708 0.001307878 0.001307582 0.001307582 0.001307582 0.001307288 38 0.7726298 0.7400598 0.7397377 0.7181263 0.714758 0.3210706 0.31184 0.02908583 0.01643369 0.01234406 0.01232842 0.01225806 0.01035409 0.01002614 0.006086484 0.003930525 0.003117488 0.002968256 0.002952424 0.002380879 0.002213184 0.002145835 0.002144146 0.002144146 0.001785204 0.00149268 0.001308559 0.001307795 0.001307512 0.001307512 0.001307512 39 0.8346883 0.7724098 0.7400116 0.7396905 0.7180912 0.714728 0.3210555 0.3118273 0.02907325 0.01643174 0.01234217 0.01232653 0.01225617 0.01035249 0.01002454 0.006085186 0.003930138 0.003117322 0.00296809 0.002952324 0.002380779 0.002213167 0.002145818 0.002144129 0.002144129 0.001785188 0.001492665 0.001308543 0.00130778 0.001307497 0.001307497 40 0.9997527 0.8344672 0.7723556 0.7399744 0.7396542 0.7180676 0.7147051 0.3210475 0.3118213 0.02906734 0.01643131 0.01234176 0.01232612 0.01225576 0.01035225 0.01002431 0.00608504 0.003930037 0.003117254 0.002968023 0.002952282 0.002380737 0.002213156 0.002145807 0.002144118 0.002144118 0.001785177 0.001492654 0.001308533 0.00130777 0.001307486 |
#energy necessary to unpair as well as to unpair if i-1 is unpaired also, if i+1 is unpaired also in dekacal/mol 1 20 -0 3 2 18 1 0 3 29 11 6 4 42 19 30 5 18 6 0 6 22 3 2 7 26 7 21 8 7 1 5 9 1 0 0 10 25 23 1 11 40 17 0 12 56 17 26 13 53 23 22 14 41 9 37 15 4 0 5 16 36 38 0 17 43 6 4 18 39 0 1 19 38 0 18 20 75 55 78 21 37 41 1 22 36 0 10 23 33 7 11 24 23 1 19 25 4 0 0 26 4 1 4 27 2 2 4 28 34 36 0 29 141 107 26 30 195 79 81 31 148 35 139 32 55 46 22 33 47 13 45 34 1 0 1 35 3 3 1 36 8 6 0 37 18 10 2 38 15 0 4 39 11 0 11 40 0 0 -0 |
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 |
ovrnaduplex | RNA duplex calculation |
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 |
vrnaplot | Plot vrnafold output |
vrnasubopt | Calculate RNA suboptimals |
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