:: DESCRIPTION
Tfold is an algorithm for predicting non-coding RNA secondary structures.
::DEVELOPER
EVRY RNA – IBISC
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: 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.
:: 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
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: 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.
:: 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.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: 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.
:: 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
:: SCREENSHOTS
n/a
:: REQUIREMENTS
:: DOWNLOAD
:: 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.
:: 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
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: 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).
:: 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
:: SCREENSHOTS
:: REQUIREMENTS
:: 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.
:: DESCRIPTION
STRIDE conduct the secondary structure assignment from atomic resolution protein structures.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: 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.
:: DESCRIPTION
Palingol is a declarative programming language to describe nucleic acids’ secondary structures and to scan sequence databases.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: 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.
:: 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
:: 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.
:: 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
:: DOWNLOAD
:: 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.