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.

RiboSketch 0.8.2 – Visualization of multi-stranded RNA and DNA Secondary Structure

RiboSketch 0.8.2

:: DESCRIPTION

RiboSketch is a drawing program for the production of RNA and DNA secondary structure images.The user provides an input file (.ct, .bpseq, .dbn, or the save file type .rs) containing the sequence and base-pairing of the strand(s).

::DEVELOPER

Shapiro Group

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux/Windows/MacOsX

:: DOWNLOAD

RiboSketch

:: MORE INFORMATION

Citation:

Lu JS, Bindewald E, Kasprzak WK, Shapiro BA.
RiboSketch: versatile visualization of multi-stranded RNA and DNA secondary structure.
Bioinformatics. 2018 Dec 15;34(24):4297-4299. doi: 10.1093/bioinformatics/bty468. PMID: 29912310; PMCID: PMC6289134.

KNetFold 1.4.4b – RNA secondary structure prediction

KNetFold 1.4.4b

:: DESCRIPTION

KNetFold is a new software for predicting the consensus secondary structure for a given alignment of RNA sequences. It uses an innovative classifier system (a hierarchical network of k-nearest neighbor classifiers) to compute for each pair of alignment positions a “base pair” or “no base pair” prediction.

::DEVELOPER

Shapiro Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 KNetFold

:: MORE INFORMATION

Citation:

Bindewald, E and Shapiro B.A (2006):
RNA secondary structure prediction from sequence alignments using a network of k-nearest neighbor classifiers.
RNA. 12(3): 342-352 (2006).

MPGAfold / MPGAfold Visualizer – Massively Parallel Genetic Algorithm that Predicts RNA Secondary Structure

MPGAfold / MPGAfold Visualizer

:: DESCRIPTION

MPGAfold is a massively parallel genetic algorithm that predicts RNA secondary structure.

MPGAfold Visualizer is a Java application that allows the user to visually see an MPGAfold run.

::DEVELOPER

Shapiro Group

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/SGI/Irix

:: DOWNLOAD

MPGAfold / MPGAfold Visualizer

Citation

Kasprzak WK, Shapiro BA.
MPGAfold in dengue secondary structure prediction.
Methods Mol Biol. 2014;1138:199-224. doi: 10.1007/978-1-4939-0348-1_13. PMID: 24696339; PMCID: PMC6354254.

STRIDE – Secondary Structure Assignment from known Atomic Coordinates of Proteins

STRIDE

:: DESCRIPTION

STRIDE conduct the secondary structure assignment from atomic resolution protein structures.

::DEVELOPER

the Dmitrij Frishman lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 STRIDE

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W500-2.
STRIDE: a web server for secondary structure assignment from known atomic coordinates of proteins.
Heinig M1, Frishman D.

Palingol 1.3 – Programming Language in the Description of Nucleic Acids Secondary Structures

Palingol 1.3

:: DESCRIPTION

Palingol is a declarative programming language to describe nucleic acids’ secondary structures and to scan sequence databases.

::DEVELOPER

L’Atelier de BioInformatique

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Palingol

:: MORE INFORMATION

Citation

Billoud, B. Kontic, M. and Viari, A. (1996).
Palingol, a descriptive programming language to describe nucleic acid’s secondary structure and scan sequence databases.
Nucleic Acids Research 24(8) 1395-1404.