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.

conSSert – Consensus Secondary Structure Prediction

conSSert

:: DESCRIPTION

conSSert is a SVM-based consenus secondary structure prediction method. Predictions from four popular secondary structure models (PSSpred, PSIPRED, Raptor-X, and SPINE-X) are integrated through the use of SVM models to produce highly accurate predictions, especially with regard to Q2-EH.

::DEVELOPER

the Multi-scale Systems Engineering Laboratory (MSEL)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

conSSert: Consensus SVM model for accurate prediction of ordered secondary structure.
Kieslich CA, Smadbeck J, Khoury GA, Floudas C.
J Chem Inf Model. 2016 Feb 29.

Rnall 2.0 – RNA Local Secondary Structure Prediction

Rnall 2.0

:: DESCRIPTION

Rnall (RNA Local secondary structure prediction by Local symmetric mapping) predicts local RNA secondary structures for multiple sequences in the Fasta format or scans local secondary structure of a single genomic sequence in the Fasta format. Rnall scans the RNA sequence with a sliding window and extracts all LSS with sizes no longer than a window size using dynamic programming. Rnall has various potential applications, such as local secondary structure prediction in RNA molecules and RNA motif prediction (such as rho-independent/intrinsic terminator, riboswitch, siRNA, and viral RNA motifs).

::DEVELOPER

Systems Biology Laboratory, College of Veterinary Medicine,Mississippi State University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows /  Linux

:: DOWNLOAD

Rnall

:: MORE INFORMATION

Citation

Wan, X.-F., G. Lin, and D. Xu. 2006.
Rnall: An efficient algorithm for predicting RNA local secondary structural landscape in genomes.
Journal of Bioinformatics and Computational Biology, 4(5):1015-31.

mRNA optimiser 1.0 – Redesign mRNA Sequences to Optimise the Secondary Structure

mRNA optimiser 1.0

:: DESCRIPTION

The mRNA optimiser is a tool that redesigns a gene messenger RNA to optimise its secondary structure, without affecting the polypeptide sequence. The tool can either maximize or minimize the molecule minimum free energy (MFE), thus resulting in decreased or increased secondary structure strength.

::DEVELOPER

UA.PT Bioinformatics

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux/ Windows/MacOsX
  • Java

:: DOWNLOAD

 mRNA optimiser

:: MORE INFORMATION

Citation

P. Gaspar, G. Moura, M. A. S. Santos, and J. L. Oliveira
mRNA secondary structure optimization using a correlated stem–loop prediction
Nucleic Acids Research, Jan 2013, doi: 10.1093/nar/gks1473

RNAfamily – Java Viewer for RNA Secondary Structures

RNAfamily

:: DESCRIPTION

RNAfamily is a simple software tools that enables to display all secondary structures of a family of RNA molecules. It uses the linear backbone representation. RNAfamily provides usual graphical features: zooming, scrolling, etc. Colors of the stems correspond to matching stems. It is also possible to display the nucleotides composing a stem or the whole sequence.

::DEVELOPER

Bonsai Bioinformatics – INRIA

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • Java

:: DOWNLOAD

RNAfamily

:: MORE INFORMATION

For questions about RNAfamily or for bug reports, please contact Helene Touzet

Carnac 0.98 – Predict Secondary Structure for a set of Homologous RNA Sequences

Carnac 0.98

:: DESCRIPTION

Carnac is a software tool for analysing the hypothetical secondary structure of a family of homologous RNA. It aims at predicting if the sequences actually share a common secondary structure. When this structure exists, Carnac is then able to correctly recover a large amount of the folded stems. The input is a set of single-stranded RNA sequences that need not to be aligned. The folding strategy relies on a thermodynamic model with energy minimization. It combines information coming from locally conserved elements of the primary structure and mutual information between sequences with covariations too.

::DEVELOPER

Bonsai Bioinformatics – INRIA

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows /  Linux / MacOsX
  • C Complier

:: DOWNLOAD

Carnac

:: MORE INFORMATION

Citation

CARNAC: folding families of related RNAs
Touzet H. and Perriquet O.
Nucl. Acids Res. (2004) 32 (suppl 2): W142-W145