RnaViz 2.0.3 – Secondary Structure Drawings of RNA Molecules

RnaViz 2.0.3

:: DESCRIPTION

RnaViz is a user-friendly, portable, GUI program for producing publication-quality secondary structure drawings of RNA molecules. Drawings can be created starting from DCSE alignment files if they incorporate structure information or from mfold ct files. The layout of a structure can be changed easily. Display of special structural elements such as pseudo-knots or unformatted areas is possible. Sequences can be automatically numbered, and several other types of labels can be used to annotate particular bases or areas. Although the program does not try to produce an initially non-overlapping drawing, the layout of a properly positioned structure drawing can be applied to newly created drawing using skeleton files. In this way a range of similar structures can be drawn with a minimum of effort. Skeletons for several types of RNA molecule are included with the program.

::DEVELOPER

Peter De Rijk

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

RnaViz

:: MORE INFORMATION

Citation

Peter De Rijk, Jan Wuyts and Rupert De Wachter (2003)
RnaViz2: an improved representation of RNA secondary structure.
Bioinformatics 19(2): 299-300

XRNA 2.0 – Creation, Annotation & Display of RNA Secondary Structure Diagrams

XRNA 2.0

:: DESCRIPTION

XRNA is a Java based suite of tools for the creation, annotation and display of RNA secondary structure diagrams.XRNA provides editing tools for easy modification of publication quality secondary diagrams that can be either drawn manually, or through automatic generation. Other features include grouping, numbering and structure annotation. XRNA secondary structures may be saved in a native format, or exported as postscript for printing and further manipulation in programs such as Adobe Illustrator.

::DEVELOPER

RNA Center, UCSC

:: SCREENSHOTS


:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • Perl

:: DOWNLOAD

XRNA

:: MORE INFORMATION

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.