                                 ovrnalfold



Wiki

   The master copies of EMBOSS documentation are available at
   http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki.

   Please help by correcting and extending the Wiki pages.

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:6.6.0.0

   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
   -scircular1         boolean    Sequence is circular
   -squick1            boolean    Read id and sequence only
   -sformat1           string     Input sequence format
   -iquery1            string     Input query fields or ID list
   -ioffset1           integer    Input start position offset
   -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


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   Ensembl-Gn; ENSG00000176890; Homo_sapiens.
DR   Ensembl-Tr; ENST00000323274; Homo_sapiens.
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"


  [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) 184
50
.(((((((....))))))) ( -4.60) 18439
.((((((......(((((((....))))))).((((((((....(((..((.((((((((((((((......))))..))
)))))))).)).....(((.(..(((......)))..).)))....)))))))))))...)))))) (-35.60) 1842
7
.((((.....)))). ( -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) 1
8328
.((((((........((((....))))....((((((((((.((.........))))))))))))..)))))). (-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) 182
59
.(((((...(((....)))..))))). (-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)  2
64
.((..(((((......(((.....))).....(((((...(((.......)))...))))).)))))...)). (-16.2
0)  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
.((((.(((.(((((.(....).))))).))).)))). (-18.40)    1
[encoded data, 18792 characters]
GGGCUUGGGGUUUUUUUGGCAGGUAGGGUUGGGAGG
 (-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        Find inverted repeats in nucleotide sequences
   ovrnaalifold     Calculate secondary structures for a set of aligned RNAs
   ovrnaalifoldpf   Calculate secondary structures for a set of aligned RNAs
                    (partition)
   ovrnacofold      Calculate secondary structures of RNA dimers
   ovrnacofoldconc  Calculate secondary structures of RNA dimers
                    (concentrations)
   ovrnacofoldpf    Calculate secondary structures of RNA dimers
                    (partitioning)
   ovrnadistance    Calculate distances between RNA secondary structures
   ovrnaduplex      Predict RNA duplex (hybridization) sites and structure
   ovrnaeval        Calculate energy of RNA sequences with a given secondary
                    structure
   ovrnaevalpair    Calculate energy of RNA sequences on given secondary
                    structure
   ovrnafold        Calculate min. energy RNA structure / pair probabilities
                    (partition)
   ovrnafoldpf      Calculate min. energy RNA structure / pair probabilities
   ovrnaheat        Calculate specific heat of RNA melting
   ovrnainverse     Find RNA sequences with a given secondary structure
   ovrnaplot        Draw RNA secondary structures
   ovrnasubopt      Calculate suboptimal secondary structure of RNA
   sirna            Find siRNA duplexes in mRNA
   vrna2dfold       Calculate RNA structures and samples of k,l neighbourhoods
   vrnaaliduplex    RNA duplex calculation for two sequence alignments
   vrnaalifold      Calculate secondary structures for a set of aligned RNAs
   vrnaalifoldpf    Calculate secondary structures for a set of aligned RNAs
                    (partition)
   vrnacofold       Calculate secondary structures of RNA dimers
   vrnacofoldconc   Calculate secondary structures of RNA dimers
                    (concentrations)
   vrnacofoldpf     Calculate secondary structures of RNA dimers
                    (partitioning)
   vrnadistance     Calculate distances between RNA secondary structures
   vrnaduplex       Predict RNA duplex (hybridization) sites and structure
   vrnaeval         Calculate energy of RNA sequences with a given secondary
                    structure
   vrnaevalpair     Calculate energy of RNA sequences on given secondary
                    structure
   vrnafold         Calculate min. energy RNA secondary structures and pair
                    probabilities
   vrnafoldpf       Calculate min. energy RNA structures / pair probabilities
                    (partition)
   vrnaheat         Calculate specific heat of RNA melting
   vrnainverse      Find RNA sequences with a given secondary structure
   vrnalalifoldpf   Calculate secondary structures for a set of aligned RNAs
                    (partition)
   vrnalfold        Calculate locally stable secondary structures of RNAs
   vrnalfoldz       Calculate locally stable secondary structures of RNAs plus
                    zscore
   vrnapkplex       Calculate RNA structures plus pseudoknots
   vrnaplfold       Compute avg. pair probabilities for local base pairs in RNA
                    sequences
   vrnaplot         Draw RNA secondary structures
   vrnasubopt       Calculate suboptimal secondary structures of RNAs

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 (c) 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
