RNA sTructure prediction using IP Scheme

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Update History

• The IPknot server has been updated to version 1.3.1. (2014-03-10)
  • The ViennaRNA package used as a background module has been updated from version 2.1.3 to 2.1.6.
• The RactIP server has been updated to version 1.2.1. (2014-03-10)
  • The ViennaRNA package used as a background module has been updated from version 2.1.3 to 2.1.6.
• The IPknot server was updated to version 1.3.0. (2013-08-27)
  • The ViennaRNA package used as a background module was updated from version 1.8.5 to 2.1.3.
• The RactIP server was updated to version 1.2.0. (2013-08-27)
  • The ViennaRNA package used as a background module was updated from version 1.8.5 to 2.1.3.
• The Perl template programs to access web services have been improved in usability. (2012-12-10)
• The server was replaced with a more high-performance machine. (2012-11-09)
• The RactIP web server was updated to version 1.1.6. (2012-09-11)
  • The present server can generate a BPSEQ formatted file for a predicted joint structure.
• The IPknot web server was updated to version 1.2.1. (2012-04-19)
  • Weights for true base pairs are limited to be at most 50 to work threshold cut properly.
  • A more strict error checking program on CLUSTAL W input has been implemented.
  • The help page has been modified.
• The RactIP web server was updated to version 1.1.5. (2012-04-19)
  • Weights for true base pairs are limited to be at most 50 to work threshold cut properly.
  • The help page has been modified.
• The IPknot web server was updated to version 1.2.0. (2012-04-03)
  • A multiple FASTA formatted input is supported for consensus structure prediction.
  • The output of consensus structure prediction indicates input alignments followed by the common structure.
  • The consensus structure in dot-bracket representation together with respective input sequences in FASTA format is downloadable.
  • A predicted structure is available as a BPSEQ file.
  • Arc representation of a predicted structure includes 5' --> 3' at the bottom to show the orientation of the RNA sequence.
  • A more strict error checking program was implemented.
  • The help page was modified.
  • A help icon close to each option was added to explain details of that specific option.
• The RactIP web server was updated to version 1.1.4. (2012-04-03)
  • Arc representation of a predicted joint structure includes 5' --> 3' at the bottom to show the orientation of each RNA sequence.
  • A more strict error checking program was implemented.
  • The help page was modified.
  • A help icon close to each option was added to explain details of that specific option.
• The IPknot web server was updated to version 1.1.4. (2012-01-24)
  • A sample input sequence changed.
  • Default weight parameters were adjusted to produce more reliable predictions.
• The IPknot web server was updated to version 1.1.3. (2011-12-28)
  • Some bugs were fixed to appropriately display dot-bracket representation with Chrome.
• The RactIP web server was updated to version 1.1.3. (2011-12-28)
  • Some bugs were fixed to appropriately display dot-bracket representation with Chrome.
• The IPknot web server was updated to version 1.1.2. (2011-12-06)
  • A Perl template program was provided to access the web server IPknot and parse the output.
  • Some bugs were fixed to enhance security.
• The RactIP web server was updated to version 1.1.2. (2011-12-06)
  • A Perl template program was provided to access the web server RactIP and parse the output.
  • Some bugs were fixed to enhance security.
• The IPknot web server was updated to version 1.1.1. (2011-11-24)
  • A help page was added.
• The RactIP web server was updated to version 1.1.1. (2011-11-24)
  • A help page was added.
• The IPknot web server was updated to version 1.1.0. (2011-11-18)
  • A predicted structure in arc representation is shown in the Results page.
  • Both 2D diagram and arc representation are downloadable as PDF files.
• The RactIP web server was updated to version 1.1.0. (2011-11-17)
  • The previous 2D diagram of a joint structure was replaced with arc representation.
  • The drawing of a predicted structure can be available in PDF format.
• The RactIP web server was updated to version 1.0.2. (2011-06-22)
  • Free energy of a predicted joint structure is displayed in the Results page.
• The IPknot web server was updated to version 1.0.3. (2011-03-24)
  • Some bugs were fixed to work the NUPACK model.
• The IPknot web server was updated to version 1.0.2. (2011-02-09)
  • Choice of refinement is not allowed for the NUPACK model.
• The IPknot web server was updated to version 1.0.1. (2011-02-01)
  • The NUPACK model was added to accurately predict pseudoknotted structures for short RNA sequences.
  • Users can choose whether or not the algorithm refines probability parameters.
• The RactIP web server was updated to version 1.0.1. (2011-02-01)
  • Choice of two prediction models (joint structure or binding site) was removed.
• The Rtips web server became available (version 1.0.0). (2010-12-03)