ViennaRNA 2.5.0 – RNA Secondary Structure Prediction & Comparison

ViennaRNA 2.5.0

:: DESCRIPTION

ViennaRNA Package consists of a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures.

Vienna RNA WebServers

::DEVELOPER

Theoretical Biochemistry Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Mac OsX/ Windows

:: DOWNLOAD

Vienna RNA

:: MORE INFORMATION

Citation

Methods Mol Biol. 2015;1269:307-26. doi: 10.1007/978-1-4939-2291-8_19.
The ViennaRNA web services.
Gruber AR1, Bernhart SH, Lorenz R.

Ivo L. Hofacker
Vienna RNA secondary structure serverNucl.
Acids Res. (2003) 31 (13): 3429-3431

Lorenz, Ronny and Bernhart, Stephan H. and Höner zu Siederdissen, Christian and Tafer, Hakim and Flamm, Christoph and Stadler, Peter F. and Hofacker, Ivo L.
ViennaRNA Package 2.0
Algorithms for Molecular Biology, 6:1 26, 2011, doi:10.1186/1748-7188-6-26

Context Fold 1.0 – RNA Secondary Structure Prediction tool

Context Fold 1.0

:: DESCRIPTION

Context Fold is an RNA secondary structure prediction tool. It applies feature-rich scoring models, whose parameters were obtained after training on comprehensive datasets.

::DEVELOPER

Michal Ziv-Ukelson’s Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac / Windows
  • Java

:: DOWNLOAD

 Context Fold

:: MORE INFORMATION

Citation

Shay Zakov, Yoav Goldberg, Michael Elhadad and Michal Ziv-Ukelson.
Rich Parameterization Improves RNA Structure Prediction
Journal of Computational Biology, November 2011, 18(11): 1525-1542. doi:10.1089/cmb.2011.0184.

ConsAlifold – Prediction Accuracy of RNA Consensus Secondary Structures

ConsAlifold

:: DESCRIPTION

ConsAlifold is a dynamic programming-based method that predicts the consensus secondary structure of an RNA sequence alignment.

::DEVELOPER

ConsAlifold team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • Python

:: DOWNLOAD

ConsAlifold

:: MORE INFORMATION

Citation

Tagashira M, Asai K.
ConsAlifold: Considering RNA Structural Alignments Improves Prediction Accuracy of RNA Consensus Secondary Structures.
Bioinformatics. 2021 Oct 25:btab738. doi: 10.1093/bioinformatics/btab738. Epub ahead of print. PMID: 34694364.

NetCSSP 20200622 – Neural networks for calculating Contact-dependent Secondary Structure Propensity

NetCSSP 20200622

:: DESCRIPTION

NetCSSP is an applications in predicting non-native secondary structures and amyloid fibril formation.

::DEVELOPER

Lab of Bioinformatics and Molecular Design

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

 :: MORE INFORMATION

Citation

Nucleic Acids Res. 2009 Jul;37(Web Server issue):W469-73. doi: 10.1093/nar/gkp351. Epub 2009 May 25.
NetCSSP: web application for predicting chameleon sequences and amyloid fibril formation.
Kim C, Choi J, Lee SJ, Welsh WJ, Yoon S.

RNAlign2D – Multiple Sequence Alignment of RNA using MUSCLE and Secondary Structure data

RNAlign2D

:: DESCRIPTION

RNAlign2D is a Python wrapper allowing one to align multiple RNA molecules using information about secondary structure and sequence. For this purpose MUSCLE program is used, but one can adjust it to use any other multiple sequence alignment tool.

::DEVELOPER

RNA Bioscience Initiative

:: REQUIREMENTS

  • Linux / MacOsX
  • Python
  • MUSCLE

:: DOWNLOAD

RNAlign2D

:: MORE INFORMATION

Citation

Woźniak T, Sajek M, Jaruzelska J, Sajek MP.
RNAlign2D: a rapid method for combined RNA structure and sequence-based alignment using a pseudo-amino acid substitution matrix.
BMC Bioinformatics. 2021 Oct 16;22(1):504. doi: 10.1186/s12859-021-04426-8. PMID: 34656080; PMCID: PMC8520625.

RNAstructure 6.3 – Prediction & Analysis of RNA Secondary Structure

RNAstructure 6.3

:: DESCRIPTION

RNAstructure is a complete package for RNA and DNA secondary structure prediction and analysis. It includes algorithms for secondary structure prediction, including facility to predict base pairing probabilities. It also can be used to predict bimolecular structures and can predict the equilibrium binding affinity of an oligonucleotide to a structured RNA target. This is useful for siRNA design. It can also predict secondary structures common to two, unaligned sequences, which is much more accurate than single sequence secondary structure prediction. Finally, RNAstructure can take a number of different types of experiment mapping data to constrain or restrain structure prediction. These include chemical mapping, enzymatic mapping, NMR, and SHAPE data.

::DEVELOPER

Mathews Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Mac / Windows
  • Java

:: DOWNLOAD

RNAstructure

:: MORE INFORMATION

Citation

AccessFold: Predicting RNA-RNA Interactions with Consideration for Competing Self-Structure.
DiChiacchio L, Sloma MF, Mathews DH.
Bioinformatics. 2015 Nov 20. pii: btv682.

Reuter, J. S., & Mathews, D. H. (2010).
RNAstructure: software for RNA secondary structure prediction and analysis.
BMC Bioinformatics. 11,129.

jViz.Rna 4.0 – Visual Comparison of RNA Secondary Structure

jViz.Rna 4.0

:: DESCRIPTION

jViz.Rna is a multi-platform visualization tool capable of displaying and comparing RNA secondary structures encoded in a number of file formats. Structures can be shown using six different visualization modes including a numerical analysis mode which includes sensitivity and specificity. Any of the drawings and data produced can be saved in a variety of formats enabling easy usage in publications and presentations.

::DEVELOPER

jViz.Rna Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Java

:: DOWNLOAD

 jViz.Rna

:: MORE INFORMATION

Citation:

Shabash B, Wiese KC.
jViz.RNA 4.0-Visualizing pseudoknots and RNA editing employing compressed tree graphs.
PLoS One. 2019 May 6;14(5):e0210281. doi: 10.1371/journal.pone.0210281. PMID: 31059508; PMCID: PMC6502502.

Kay C. Wiese and Edward Glen (2006),
jViz.Rna – An Interactive Graphical Tool for Visualizing RNA Secondary Structure Including Pseudoknots
Proceedings of the 19th International Symposium on Computer Based Medical Systems (IEEE/CBMS-2006), June 2006, pp 659-664.

TFold – RNA Secondary Structure Prediction

TFold

:: DESCRIPTION

Tfold is an algorithm for predicting non-coding RNA secondary structures.

::DEVELOPER

EVRY RNA – IBISC

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2010 Apr;38(7):2453-66. doi: 10.1093/nar/gkp1067. Epub 2010 Jan 4.
Tfold: efficient in silico prediction of non-coding RNA secondary structures.
Engelen S1, Tahi F.

RactIP 2.1.0 – Joint Secondary Structure Prediction

RactIP 2.1.0

:: DESCRIPTION

RactIP provides services for predicting RNA joint secondary structures under the general type of interaction including kissing hairpins. RactIP runs fast and predicts the maximum expected accuracy (MEA) structure using integer programming (IP) with threshold cut.  RactIP can integrate approximate information on an ensemble of equilibrium joint structures into the objective function of integer programming using posterior internal and external base-paring probabilities.

::DEVELOPER

Yuki KatoKengo Sato.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 RactIP

:: MORE INFORMATION

Citation

Y. Kato, K. Sato, K. Asai and T. Akutsu,
Rtips: fast and accurate tools for RNA 2D structure prediction using integer programming,
Nucleic Acids Res., 40, W29-W34, 2012

Y. Kato, K. Sato, M. Hamada, Y. Watanabe, K. Asai and T. Akutsu,
RactIP: fast and accurate prediction of RNA-RNA interaction using integer programming,
Bioinformatics, vol. 26, no. 18, pp. i460-i466, 2010.

CONTRAfold 2.02 – RNA Secondary Structure Prediction

CONTRAfold 2.02

:: DESCRIPTION

CONTRAfold is a novel secondary structure prediction method based on conditional log-linear models (CLLMs), a flexible class of probabilistic models which generalize upon SCFGs by using discriminative training and feature-rich scoring. By incorporating most of the features found in typical thermodynamic models, CONTRAfold achieves the highest single sequence prediction accuracies to date, outperforming currently available probabilistic and physics-based techniques. Our result thus closes the gap between probabilistic and thermodynamic models, demonstrating that statistical learning procedures provide an effective alternative to empirical measurement of thermodynamic parameters for RNA secondary structure prediction.

CONTRAfold Online Version 

::DEVELOPER

Serafim’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 CONTRAfold

:: MORE INFORMATION

Citation

Do, C.B., Woods,D.A., and Batzoglou, S. (2006)
CONTRAfold: RNA Secondary Structure Prediction without Energy-Based Models.
Bioinformatics, 22(14): e90-e98.