ovrnalfold

 

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Function

Calculate locally stable secondary structures of RNAs

Description

This is a port of the Vienna RNA package program RNAlfold.

It reads RNA sequences, calculates their minimum free energy (mfe) structure and prints the mfe structure in bracket notation and its free energy. Optionally it also computes the partition function (pf) and base pairing probability matrix, and prints the free energy of the thermodynamic ensemble, the frequency of the mfe structure in the ensemble, and the ensemble diversity.

Algorithm

See the original documentation for the Vienna RNA package http://www.tbi.univie.ac.at/~ivo/RNA/

Usage

Here is a sample session with ovrnalfold 


% ovrnalfold 
Calculate locally stable secondary structures of RNAs
Input nucleotide sequence: tembl:d00596
Vienna RNALfold output file [d00596.ovrnalfold]:

Go to the input files for this example
Go to the output files for this example

Command line arguments 

Calculate locally stable secondary structures of RNAs
Version: EMBOSS:6.4.0.0

   Standard (Mandatory) qualifiers:
  [-sequence]          sequence   Nucleotide sequence filename and optional
                                  format, or reference (input USA)
  [-outfile]           outfile    [*.ovrnalfold] Vienna RNALfold output file

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers:
   -constraintfile     infile     Vienna RNA structure constraints file
                                  (optional)
   -paramfile          infile     Vienna RNA parameters file (optional)
   -separation         integer    [150] Maximum allowed separation (Any
                                  integer value)
   -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
   -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 (Ignore); 1 (Only
                                  unpaired bases for just one dangling end); 2
                                  (Always use dangling energies); 3 (Allow
                                  coaxial stacking of adjacent helices))

   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

   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 RNALfold output file Output file <*>.ovrnalfold
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
-separation integer Maximum allowed separation Any integer value 150
-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
-energy list Rarely used option to fold sequences from the ABCD... alphabet
0 (BP)
1 (Any with GC)
2 (Any with AU parameters)
 0
-dangles list Method
0 (Ignore)
1 (Only unpaired bases for just one dangling end)
2 (Always use dangling energies)
3 (Allow coaxial stacking of adjacent helices)
 1
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  
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

Input file format

ovrnalfold reads any normal sequence USAs.

Input files for usage example

'tembl:d00596' is a sequence entry in the example nucleic acid database 'tembl'

Database entry: tembl:d00596

ID   D00596; SV 1; linear; genomic DNA; STD; HUM; 18596 BP.
XX
AC   D00596;
XX
DT   17-JUL-1991 (Rel. 28, Created)
DT   07-DEC-2007 (Rel. 94, Last updated, Version 6)
XX
DE   Homo sapiens gene for thymidylate synthase, complete cds.
XX
KW   .
XX
OS   Homo sapiens (human)
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC   Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae;
OC   Homo.
XX
RN   [1]
RP   1-18596
RX   PUBMED; 2243092.
RA   Kaneda S., Nalbantoglu J., Takeishi K., Shimizu K., Gotoh O., Seno T.,
RA   Ayusawa D.;
RT   "Structural and functional analysis of the human thymidylate synthase
RT   gene";
RL   J. Biol. Chem. 265(33):20277-20284(1990).
XX
DR   GDB; 163670.
DR   GDB; 182340.
XX
CC   These data kindly submitted in computer readable form by:
CC   Sumiko Kaneda
CC   National Institute of Genetics
CC   1111 Yata
CC   Mishima 411
CC   Japan
XX
FH   Key             Location/Qualifiers
FH
FT   source          1..18596
FT                   /organism="Homo sapiens"
FT                   /chromosome="18"
FT                   /map="18p11.32"
FT                   /mol_type="genomic DNA"
FT                   /clone="lambdaHTS-1 and lambdaHTS-3"
FT                   /db_xref="taxon:9606"
FT   repeat_region   1..148
FT                   /rpt_family="Alu"
FT   repeat_region   202..477
FT                   /rpt_family="Alu"
FT   prim_transcript 822..16246
FT                   /note="thymidylate synthase mRNA and introns"


  [Part of this file has been deleted for brevity]

     ttttgttttt agcttcagcg agaacccaga cctttcccaa agctcaggat tcttcgaaaa     15660
     gttgagaaaa ttgatgactt caaagctgaa gactttcaga ttgaagggta caatccgcat     15720
     ccaactatta aaatggaaat ggctgtttag ggtgctttca aaggagctcg aaggatattg     15780
     tcagtcttta ggggttgggc tggatgccga ggtaaaagtt ctttttgctc taaaagaaaa     15840
     aggaactagg tcaaaaatct gtccgtgacc tatcagttat taatttttaa ggatgttgcc     15900
     actggcaaat gtaactgtgc cagttctttc cataataaaa ggctttgagt taactcactg     15960
     agggtatctg acaatgctga ggttatgaac aaagtgagga gaatgaaatg tatgtgctct     16020
     tagcaaaaac atgtatgtgc atttcaatcc cacgtactta taaagaaggt tggtgaattt     16080
     cacaagctat ttttggaata tttttagaat attttaagaa tttcacaagc tattccctca     16140
     aatctgaggg agctgagtaa caccatcgat catgatgtag agtgtggtta tgaactttaa     16200
     agttatagtt gttttatatg ttgctataat aaagaagtgt tctgcattcg tccacgcttt     16260
     gttcattctg tactgccact tatctgctca gttccttcct aaaatagatt aaagaactct     16320
     ccttaagtaa acatgtgctg tattctggtt tggatgctac ttaaaagagt atattttaga     16380
     aataatagtg aatatatttt gccctatttt tctcatttta actgcatctt atcctcaaaa     16440
     tataatgacc atttaggata gagttttttt tttttttttt taaactttta taaccttaaa     16500
     gggttatttt aaaataatct atggactacc attttgccct cattagcttc agcatggtgt     16560
     gacttctcta ataatatgct tagattaagc aaggaaaaga tgcaaaacca cttcggggtt     16620
     aatcagtgaa atatttttcc cttcgttgca taccagatac ccccggtgtt gcacgactat     16680
     ttttattctg ctaatttatg acaagtgtta aacagaacaa ggaattattc caacaagtta     16740
     tgcaacatgt tgcttatttt caaattacag tttaatgtct aggtgccagc ccttgatata     16800
     gctatttttg taagaacatc ctcctggact ttgggttagt taaatctaaa cttatttaag     16860
     gattaagtag gataacgtgc attgatttgc taaaagaatc aagtaataat tacttagctg     16920
     attcctgagg gtggtatgac ttctagctga actcatcttg atcggtagga ttttttaaat     16980
     ccatttttgt aaaactattt ccaagaaatt ttaagccctt tcacttcaga aagaaaaaag     17040
     ttgttggggc tgagcactta attttcttga gcaggaagga gtttcttcca aacttcacca     17100
     tctggagact ggtgtttctt tacagattcc tccttcattt ctgttgagta gccgggatcc     17160
     tatcaaagac caaaaaaatg agtcctgtta acaaccacct ggaacaaaaa cagattttat     17220
     gcatttatgc tgctccaaga aatgctttta cgtctaagcc agaggcaatt aattaatttt     17280
     tttttttttg acatggagtc actgtccgtt gcccaggctg cagtgcagtg gcgcaatctt     17340
     ggctcactgc aacctccacc tcccaggttc aagtgattct cctgcctcag cctcccatgt     17400
     agctgggatc acaggcacct gccaccatgc ccggctaatt ttttgtattt tttgtagaga     17460
     cagggtttca ccatgttggc caggctggtc tcaaacacct gacctcaaat gatccacctg     17520
     cctcagcctc ccaaagtgtt gggattacag gcgtaagcca ccatgcccag ccctgaatta     17580
     atatttttaa aataagtttg gagactgttg gaaataatag ggcagaggaa catattttac     17640
     tggctacttg ccagagttag ttaactcatc aaactctttg ataatagttt gacctctgtt     17700
     ggtgaaaatg agccatgatc tcttgaacat gatcagaata aatgccccag ccacacaatt     17760
     gtagtccaaa ctttttaggt cactaacttg ctagatggtg ccaggttttt ttgcacaagg     17820
     agtgcaaatg ttaagatctc cactagtgag gaaaggctag tattacagaa gccttgtcag     17880
     aggcaattga acctccaagc cctggccctc aggcctgagg attttgatac agacaaactg     17940
     aagaaccgtt tgttagtgga tattgcaaac aaacaggagt caaagcttgg tgctccacag     18000
     tctagttcac gagacaggcg tggcagtggc tggcagcatc tcttctcaca ggggccctca     18060
     ggcacagctt accttgggag gcatgtagga agcccgctgg atcatcacgg gatacttgaa     18120
     atgctcatgc aggtggtcaa catactcaca caccctagga ggagggaatc agatcggggc     18180
     aatgatgcct gaagtcagat tattcacgtg gtgctaactt aaagcagaag gagcgagtac     18240
     cactcaattg acagtgttgg ccaaggctta gctgtgttac catgcgtttc taggcaagtc     18300
     cctaaacctc tgtgcctcag gtccttttct tctaaaatat agcaatgtga ggtggggact     18360
     ttgatgacat gaacacacga agtccctctg agaggttttg tggtgccctt taaaagggat     18420
     caattcagac tctgtaaata tccagaatta tttgggttcc tctggtcaaa agtcagatga     18480
     atagattaaa atcaccacat tttgtgatct atttttcaag aagcgtttgt attttttcat     18540
     atggctgcag cagctgccag gggcttgggg tttttttggc aggtagggtt gggagg         18596
//

Output file format

ovrnalfold outputs a graph to the specified graphics device. outputs a report format file. The default format is ...

Output files for usage example

File: d00596.ovrnalfold

.((((..((.......))..)))). ( -3.80) 18572
.(((((((((((.....))..))))))))). (-11.00) 18553
.((((..(((((((((((.....))..))))))))).....)))). (-13.60) 18547
.((..((..((.((((...((((.((((....))))))))......)))).))....))..)). (-14.60) 18533
.(((.(..(((......)))..).))).....(((((((((((.....))..))))))))). (-15.60) 18522
.((..(((...(((.(..(((......)))..).))).....(((((((((((.....))..)))))))))......)))..)). (-19.10) 18512
.(((.((((((............(((.(..(((......)))..).))).....(((((((((((.....))..)))))))))...)))))).))). (-20.30) 18500
.(((.....)))......((..(((...(((.(..(((......)))..).))).....(((((((((((.....))..)))))))))......)))..)). (-21.00) 18495
.(((((........)))))....((..(((...(((.(..(((......)))..).))).....(((((((((((.....))..)))))))))......)))..)). (-22.00) 18490
.(((((((((((((......))))..)))))))))(..(((...(((.(..(((......)))..).))).....(((((((((((.....))..)))))))))......)))..). (-23.20) 18479
.((.((((((((((((((......))))..)))))))))).)).....(((.(..(((......)))..).))).....(((((((((((.....))..))))))))). (-24.50) 18475
.(((((.(((((.((((((((.....(((.....))).(((........)))....)))).)))).))))).))))).((((..(((((((((((.....))..))))))))).....)))). (-26.20) 18470
.((..((.((.((.((((((((((((((......))))..)))))))))).)).....(((.(..(((......)))..).))).....(((((((((((.....))..)))))))))...)).))..)). (-26.90) 18465
.((((((.((((((((...((.((((((((((((((......))))..)))))))))).))...((((...((........))..((((.((....)).))))...))))......)))))))).)).)))). (-31.50) 18457
.((..((..((((((((....(((..((.((((((((((((((......))))..)))))))))).)).....(((.(..(((......)))..).)))....)))))))))))))..))...((((..((.......))..)))). (-32.80) 18450
.(((((((....))))))) ( -4.60) 18439
.((((((......(((((((....))))))).((((((((....(((..((.((((((((((((((......))))..)))))))))).)).....(((.(..(((......)))..).)))....)))))))))))...)))))) (-35.60) 18427
.((((.....)))). ( -4.70) 18405
.((((.((((.....)))))))). ( -7.50) 18400
.((((......((((.((((.....)))))))).......)))). (-12.42) 18390
.((((((..(((.(((........))))))....)))))). (-12.60) 18381
.(((((((((..(((.(((........))))))....))))))...))). (-13.80) 18378
.((((((...((((...))))...(((((((((((.....)))).((.(((((...((((.......(((((...((....))...)))))........))))))))).)).......))))))).)))))). (-34.36) 18375
.(((...(((((((..((((...)))))))))))...((((.....)))).))). (-14.60) 18369
((..(((...(((((((..((((...)))))))))))...((((.....)))).)))..)). (-15.00) 18366
.(((..(((...(((((((..((((...)))))))))))...((((.....)))).)))..))) (-15.20) 18364
.(((((.......((.(((((((..((((...))))))))))))).((((.....))))))))). (-15.30) 18360
.((((((((((.((.........)))))))))))). (-14.00) 18353
.((.((((((((((.((.........)))))))))))))). (-14.50) 18350
.((((....)))). ( -1.00) 18337
.(((((....((((....))))....((((((((((.((.........))))))))))))...))))). (-18.90) 18328
.((((((........((((....))))....((((((((((.((.........))))))))))))..)))))). (-19.50) 18323
.(((((((((.........((((....))))....((((((((((.((.........))))))))))))..(((.(((........))))))..))))))))). (-28.60) 18319
.(((.((((.((((((.........((((....))))....((((((((((.((.........))))))))))))..)))))).)))).))). (-27.40) 18313
.((((((((..((((((.((.((...............))..)).)))))).(((((((((.((.........)))))))))))....)))))))). (-30.56) 18303
.((((((........(..((.((((.((((((.........((((....))))....((((((((((.((.........))))))))))))..)))))).)))).))..)........)))))). (-38.09) 18297
.(((((((...((((((((..((((((.((.((...............))..)).)))))).(((((((((.((.........)))))))))))....))))))))..((((.((((.....)))))))).....)))).))). (-43.46) 18293
.(((.(....).))). ( -2.30) 18282
.((((((((.(....).))........((((((((..((((((.((.((...............))..)).)))))).(((((((((.((.........)))))))))))....)))))))).)))))) (-36.56) 18277
.((((((..((((((((.......((((((((..(((((..(((..........................)))....))))))))))))).)))).)))))))))). (-28.87) 18272
((((((..((((......))))..)))))). ( -8.10) 18266
.((((..((((((..((((......))))..))))))........((((((((..((((((.((.((...............))..)).)))))).(((((((((.((.........)))))))))))....))))))))..)))). (-43.06) 18259
.(((((...(((....)))..))))). (-10.40) 18250
.(((.....))). ( -2.80) 18234
.(((((((((.....))).....(((((...(((....)))..)))))..........)))))). (-17.10) 18228
.(((...((...(((.....))).....(((((...(((....)))..)))))....)).))). (-18.60) 18223
((..((..((((..(((...((...(((.....))).....(((((...(((....)))..)))))....)).))).....))))..))..)). (-24.00) 18210
.((((((((..(((..........)))..)))))))). (-13.60) 18207
.((((((........((((((((..(((..........)))..)))))))).......(((((...(((....)))..))))).............))).))). (-28.40) 18193
.(((((((((.(...........((((((((..(((..........)))..)))))))).......(((((...(((....)))..)))))..........))))).))))). (-33.80) 18185


  [Part of this file has been deleted for brevity]

.(((...((....)).........((((....(((....))).....)))).))). (-14.80)  424
(((((((....((...((....))...))....))))))). ( -8.90)  415
.(((((.....(((((.......))))).((....)).......))))). ( -9.90)  402
.(((((.(.((((....)))).)......(((((..(((......................(((....)))...((.....)))))..))))).......))))). (-33.70)  395
((((..(....)..)))). ( -5.10)  393
(((((.(.((...(((((.....(((((.......))))).((....)).......))))).....(((....)))..)).).))))). (-28.50)  390
(((.((((.(((...((.(.((((....)))).).)).))).)))).))). (-19.80)  384
((.((((.(((.(((...((.(.((((....)))).).)).))).)))..((....)).........)))).)). (-22.20)  381
.(((.((((.(((.(((...((.(.((((....)))).).)).))).)))..((....)).........)))).))) (-22.40)  379
.(((((............(((.((((.(((...((.(.((((....)))).).)).))).)))).)))))))). (-29.10)  366
.(((.((((((..(((((.((..(((.(((..(((.....)))))))))..))))))).)).)))).))). (-29.90)  361
.((.(((.((((((..(((((.((..(((.(((..(((.....)))))))))..))))))).)).)))).))).)). (-30.40)  358
.((((((((.....(((((............(((.((((.(((...((.(.((((....)))).).)).))).)))).))))))))....)))))))). (-33.00)  353
(((((((..((.(((.((((((..(((((.((..(((.(((..(((.....)))))))))..))))))).)).)))).))).)).....))))))). (-35.80)  350
.(((((((.(((((((..((.(((.((((((..(((((.((..(((.(((..(((.....)))))))))..))))))).)).)))).))).)).....))))))).))))))). (-39.30)  341
.((((((..(.(((((((.(((((((..((.(((.((((((..(((((.((..(((.(((..(((.....)))))))))..))))))).)).)))).))).)).....))))))).)))))))).)))))). (-50.30)  331
.((...((((((..(.(((((((.(((((((..((.(((.((((((..(((((.((..(((.(((..(((.....)))))))))..))))))).)).)))).))).)).....))))))).)))))))).)))))).)). (-50.60)  326
.((.((...((((((..(.(((((((.(((((((..((.(((.((((((..(((((.((..(((.(((..(((.....)))))))))..))))))).)).)))).))).)).....))))))).)))))))).)))))).)).)). (-51.70)  323
.(((.......))). ( -1.10)  297
.(((((...(((.......)))...))))). ( -5.80)  289
.((((.....(((((...(((.......)))...))))).....)))). ( -8.80)  280
.(((((.((((((.....))).....(((((...(((.......)))...)))))....)))))))). (-15.10)  264
.((..(((((......(((.....))).....(((((...(((.......)))...))))).)))))...)). (-16.20)  258
.((((.((..(((((......(((.....))).....(((((...(((.......)))...))))).)))))...)))))). (-20.40)  253
.((((((.((....((((.((..(((((......(((.....))).....(((((...(((.......)))...))))).)))))...)))))).)))))))) (-30.20)  240
((......)). ( -0.20)  228
(((((.......))))). ( -6.10)  219
(((((((.......))))).)). ( -8.00)  217
.((((...(((..........................(((((((.......))))).)).((((((..(((.(((.((..((.(((((......(((.....)))...))))).))..)).)))....)))..))))))...)))..)))). (-36.40)  180
.((....)). ( -2.60)  176
.(((((((.((....)).))))))). ( -5.20)  170
.((((((....(((((((.((....)).)))))))....)))))). ( -6.00)  160
.(((.((((((....(((((((.((....)).)))))))....)))))).))). ( -6.10)  156
.((((..(((.((((((....(((((((.((....)).)))))))....)))))).)))..........(((((.......))))))))). (-19.00)  150
.(((((((((((((((((((((((((((((....(..........)....))))))))))))))))))))))))))))). (-41.90)  126
.((((((((((((((((((((((((((((((((((((....(..........)....))))))))))))))............)))))))))))))))))))))). (-50.20)  119
.(((((((((((..((((((((((((((((((((((((((((((((((....(..........)....))))))))))))))............))))))))))))))))))))))))))))))). (-64.10)  108
((.(((((((((((..((((((((((((((((((((((((((((((((((....(..........)....))))))))))))))............))))))))))))))))))))))))))))))).)). (-68.00)  106
.((((((((((((.(((((((((((..((((((((((((((((((((((((((((((((((....(..........)....))))))))))))))............))))))))))))))))))))))))))))))).)))))))))))). (-93.50)   95
.(((....))). ( -1.40)   81
.(((((((.((((....)).))))))))). (-15.50)   64
.((((..(((((((.((((....)).))))))))))))). (-21.80)   58
.((((((((..(((((((.((((....)).))))))))))))).)))) (-27.10)   54
.((((....)))). ( -2.30)   42
.((((..........((((....))))....((((..(((((((.((((....)).))))))))))))).)))) (-29.90)   28
((((...)))). ( -3.60)   25
.(((.....((((...)))).......((((....))))..))). (-10.60)   16
.(((.(((((.(....).))))).))). (-13.30)    6
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CGAAGCGGGCGGAUCACCUGAGGUCAGGAGUUCGAGGCCAGCCUGACCAACAUGGAGAAACGCUGUCUCUACUAAAAAUACAAAAUUAGCUGGGUGUAGUGGCGCAUGCCUGUAAUCCCAGCUACUCGGGAGGCUGAGGCAGGGGAAUCGCUUGAACCUGGGAGGUGGAGGGUGCCGUGAGCCACGAUCGCGCCAUUGCACUCCAGCCUGGGCAACAAGAGCGAAACUCUCAAAAAACAAAAAAAAGGAUGGGUUCCAUAUGGGUGGUGUCAAGUGCCCACCUCCUAGCAAGUCAGCAGGGGCCAGAGGCCCUUGUAAGUGGUGUCUCGGGGGGAUCAACUGAGAUGGCUUAAGAUUUACCUGGAUGCCUGCUCUGCUCUCCCCAUCUCUUCCAGGGAUCCACAAAUGCUAAAGAGCUGUCUUCCAAGGGAGUGAAAAUCUGGGAUGCCAAUGGAUCCCGAGACUUUUUGGACAGCCUGGGAUUCUCCACCAGAGAAGAAGGGGACUUGGGCCCAGUUUAUGGCUUCCAGUGGAGGCAUUUUGGGGCAGAAUACAGAGAUAUGGAAUCAGGUGAGGAGAUAGAACAAUGCCUUCCAUUUCCGGGUGCCCUUCCUAGCACGUGUUUGCUCCGUUGUUUUAGAUAAGGUCUGGGGGAUGAGUCAAUGUCACAGGAGCUGAUGUAUAGCUUUGACCUUGUGAGGGGUGGUGCCAGGUUGAAGCCACAAUUAACGCCUACUGAAGGCCGUUUCACAUCUUUUUUUUUUUUUUUUUUUUAAUUAUUAUACUUUAAGUUUUAGGGUACAUGUGCACAAUGUGCAGGUUAGUUACAUAUGUAUACAUGUGCCAUGCUGGUGCGCUGCACCACUAACUCACCAUCUAGCAUCAGGUAUAUCUCCCAAUGCUAUCCCUCCCCCCUCCUCCCACCCCACAACAUCCCCAGAGUGUGAUGUUCCCCUUCCUGUGUCCAUAUGUUCUCGUUGUUCGAUUCCCACUAUGAGUGAGAAUAUGCGGUGUUUGGUUUUUUGUUCUUGCGAUAGUUUACUGAGAAUGAUGAUUUCCAUUUCACCACGUCCCUACAGAGGACAUGAACUCAUCAUUUUUUAUGGCUGCAUAGUAUUCCAUGGUGUAUAUGUGCCACAUUUUCUUAAUCCAGUCUAUCAUGUUGGACAUUUGGGUUGGUUCCAAGUCUUUGCCUAUUGUGAAUAGUGCCACAAUAAACAUACGUGUGCAUGUGUCUUUAUAGCAGCAUGAUUUAAUAGUCCUUUGGGUAUAUACCCAGUAAUGGGAUGGCUGGGUCAAAUGGUAUUUCUAGUUCUAGAUCCCCGAGGAAUCGCCACACUGACUUCCACAAUGGUUGAACUAGUUUACAGUCCCACCAACAGUGUCAAAGUGUCCUAUUUCUCCACAUCCUCUCCAGCACCUGUUGUUUCCUGACUUUUUAAUGAUUGCCAUUCUAACUGGUGUGAGAUGGUAUCUCAUUGUGGUUUUGAUUUGCGUUUCUCUGAUGGCCAGUGAUGGUGAGCAUUUUUUCAUGUGUUUUUUGGCUGCAUAAAUGUCUUCUUUUGAGAAGUGUCUGUUCAUGUCCUUCGCCCACUUUUUGAUGGGGUUGUUUUUUUCUUAUAAAUUUGUUUGAGUUCAUUGUAGAUUCUGGAUAUUAGCCCUUUGUCAGAUGAGUAGGUUGCAAAAAUGUUCUCCCAUUUUGUGGGUUGCCUGUUCACUCUGAUGGUAGUUUCUUUUGCUGUGCAGAAGCUCUUUAGUUUAAUUAGAUCCCAUUUGUCAAUUUUGGCUUUUGUUGCCAUUGCUUUUGGCAUAGGCAUGAAGUCCUUGCCCAUGCCUAUGUCCUGAAUGGUAAUGCCUAGGUUUUCUUCUAGGGUUUUUAUGGUUUUAGGUCUAACGUUUAAGUCUUUAAUCCAUCUUGAAUUGAUUUUUGUAUAAGGUGUAAGGAAGGGAUCCAGUUUCAGCUUUUUACAUAUGGCUAGCCAGUUUUCCCAGCACCAUUUAUUACAUAGGGAAUCCUUUCCCCAUUGCUUGUUUUUCUCAGGUUUGUCAAAGAUCAGAUAGUUGUAGAUAUGCGGCGUUAUUUCUGAGGGCUCUGUUCUGUUCCAUUGAUCUAUGUGUCUGUUUUGGUACCAGUACCAUACUGUUUUGGUUACUGUAGCCUUGUAGUAUAGUUUGAAGUCAGGUAGCGUGAUGCCUCCAGCUUUGUUCUUUUGGCUUAGGAUUGACUUGGCGAUGCGGGCUCUUUUUUGGUUCCAUAUGAACUUUAAAGUAGUUUUUUCCAAUUCUGUGAAGAAAGUCAUUGGUAGCUUGAUGGGGAUGGCAUUGAAUCUAUAAAUUACCUUGGGCAGUAUGGCCAUUUUCACGAUAUUGAUUCUUCCUACCCAUGAGCAUGGAAUGGUCUUCCAUUUCUUUGUAUCCUCUUUUAUUUCAUUGAGCAGUGGUUUGUAGUUCUCCUUGAAGAGGUCCUUCACAUCCCUUUUAAGGUGGAUUCCUAGGUAUUUUAUUCUCUUUGAAGCAAUUGUGAGUGGAAGUUCACUCAUGAUUUGGCUCUCUGUUUGUCUGUUAUUGGUGUAUAAGAAUGCUUGUGAUUUUUGCAGAUUGAUUUUAUAUCCUGAGACUUUGCUGAAGCUGCUUAUCAGCUUAAGGAGAUUUUGGGCUGAGACAAUGGGGUUUUCUAGAUAUACAAUCAUGUCGUCUGCAAACAGGGACAAUUUGACUUCCUCUUUUCCUAAUUGAAUACCCUUUAUUUCCUUCUCCUGCCUAAUUGCCCUGGCCAGAACUUCCAACACUAUGUUGAAUAGGAGUGGUGAGAGAGGGCAUCCCUGUCUUGUGCCAGUUUUCAAAGGGAAUGCUUCCAGUUUUUGCCCAUUCACUAUGAUAUUGGCUGUGGCUUUGUCAUAGAUAGCUCUUAUUAUUUUGAAAUAUGUUCCAUCAAUACCUAAUUUAUUGAGAGUUUUUAGCAUGAUGUGUUGUUGAAUUUUGUCAAAGGCUUUUUCUGCAUCUAUUGAGAUAAUCAUGUGGUUUUUGUCUUUGGAUCUGUUUAUAUGCUGGAUUACAUUUAUUGAUUUGCGUAUAUUGAACCAGCCUUGCAUCCUAGGGAUGAAGCCCACAUGAUCAUGGUGGAUAAGCUUUUUGAUGUGCUGCUGGAUUCGGUUUGCCAGUAUUUUAUUGAGGAUUUUUGCAUCAAUGUUCAUCAAGGAUAUUGGUCUAAAAUUCUCUUUUUUGGUGUGUCUCUGCCCAGCUUUGGUAUCAGGAUGAUGUUGGCUUCAUAAAAUGAGUUAGGGAGGAUUCCCUCUUUUUCUAUUGAUUGGAAUAGUUUCAGAAGGAAUGGUACCAGUUCCUCUUUGUACCUCUGGAGAAUUCGGCUGUGAAUCCAUCUGGUCCUGGACUCUCUUUGGUUGGUAAGCUAUUGAUUAUUGCCACAAUUUCAGCUCCUGUUAUUGGUCUAUUCAGAGAUUCAACUUCUUCCUGGUUUAGUCUUGGGAGAGUGUAUGUGUCAAGGAAUUUAUCCAUUUCUUCUAGAUUUUCUAGUUUAUUUGCGUAGAGGUGUUUGUAGUAAUCUCUGAUGGUAGUUUGUAUUUCUGUGGGAUCGGUGGUGAUAUCCCCUUUAUCAUUUUUUAUUGCGUCUAUUUGAUUCUUCUCUUUUUCUUUAUUAGUCUUGCUAGCGGUCUAUAAAUUUUGUUGAUCCUUUCAAAAAACCAGCUCCUGGAUUCAUUAAUUUUUUGAAGGGUUUUUUGUGUCUCUAUUUCCUUCAGUUCUGCUCUGAUUUUAGUUAUUUCUUGCCUUCUGCUAGCUUUUGAAUAUGUUUGCUCUUGCUUUUCUAGUUCUUUUAAUUGUGAUGUUAGGGUGUCAAUUUUGGAUCUUUCCUGCUUUCUCUUGUGGGCAUUUAGUGCUAUAAAUUUCCCUCUACACACUGCUUUGAAUGUGUCCCAGAGGUUCUGGUAUGUUGUGUCUUUGUUCUUGUUGGUUUCAAAGAACAUCUUUAUUUCUGCCUUCAUUUCGUUAUGUACCCAGUAGUCAUUCAGGAGCAGGUUGUUCAGUUUCCAUGUAGUUGAGCAGUUUUGAGUGAGAUUCUUAAUCCUGAGUUCUAGUUUGAUUGCACUGUGGUCUGAGAGAUAGUUUGUUAUAAUUUCUGUUCUUUUACAUUUGCUGAGGAGAGCUUUACUUCCAACUAUGUGGUCGGUUUUGGAAUAGGUGUGGUGUGGUGCUGAAAAAAAUGUAUAUUCUGUUGAUUUGGGAUGGAGUUCUGUAGAUGUCUAUUAGGUCUGCUUGGUGCAGAGCUGAGUUCAAUUCCUGGGUAUCCUUGUUGACUUUCUGUCUCGUUGAUCUGUGUACUGUUGACAGUGGGUGUUAAAGUCUCCCAUUAUUAAUGUGUGGAGUCUAAGUCUCUUUGUAGGUCACUCAGAUGAUUGGCACUUACUGGGCGCUUGGCACUUUCCAUACUGUGUCAUCGGCAGAUAGCUGCAUGGUUGGUGUUCGUGCUGGGGAAUGGGAAGUUCAUCGGUGGGACAAGGACAAAAUGCCCCCAUUGCUUUGUUGUGGCUUUAAUCUCCCUUUCGAGGCUGAGCCACAGCGUGCUGUAGGUGGCGCUGCUGUGAAGCGCAGUACCAGGGUCACACUCCACUCCCAGCUCUGCAGAGGUGGAGAAAGAAUGAAACAUCUCACUCCUGGACUUCCACUUUCCUGUCACUGUUGGUGUCACCUCUUACUGGAUGUCACAGAGCCCAGCCCCUCCCACCUGUGCCUAGGAAAAGCAGAUGCCACCUUGGAAUGUGGGGUUUGUGUGUGCAAUUUACUAGCUGGGCAGAGACCAGCAACCUGGAGAGCAGGUGUCUCGUCUAAGGGGACAGUCACAUUUCACCUCCAGCCACCUGGAGGAAUUUGGGCCUGGUGAUGUCAGAAUUCUUCAAUAAAAGCCUAAAAUCUAUAUUUUAUGUGCGGUCAUGAGAUCUGUUAAAUGUUAGCAACUUCAGGAAGUUUAAAAAUGCUGUGUGGACCUA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 (-5380.12)

Data files

For details of Vienna RNA file formats, see the original documentation http://www.tbi.univie.ac.at/~ivo/RNA/

Notes

None.

References

None.

Warnings

None.

Diagnostic Error Messages

None.

Exit status

It always exits with status 0.

Known bugs

None.

See also

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
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
vrnaplfold Locally stable RNA 2ry structures - pair probabilities
vrnaplot Plot vrnafold output
vrnasubopt Calculate RNA suboptimals

Author(s)

This program is an EMBOSS conversion of a program written by Ivo Hofacker as part of his VIENNA package.

Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.

History

Converted (October 2005) by Alan Bleasby

Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.

Comments