SStructView 1.2.2 – RNA Secondary Structure Viewing Java Applet

SStructView 1.2.2

:: DESCRIPTION

SStructView is a Java applet for viewing RNA secondary structures and linking to multiple computational backends. SStructView supports colored bases, standard mouse selection mechanisms (drag to select a range, control-click to select individuals), arbitrary set-based data types to allow you to create your own groups, and other improvements.RNA biologists who want an extendible java application for viewing RNA secondary structure.

::DEVELOPER

Ramon M. Felciano, Richard Chen and Russ Altman, Helix Group

:: SCREENSHOTS

:: REQUIREMENTS

Windows / MacOsX / Linux
Java

:: DOWNLOAD

SStructView

:: MORE INFORMATION

Citation

R. M. Felciano, R. O. Chen, & R. B. Altman.
RNA Secondary Structure as a Reusable Interface to Biological Information Resources.
Gene 190 (1997) GC59-70

SSPcompare – Takes a Library of known RNA Sequence-structure Pairs

SSPcompare

:: DESCRIPTION

SSPcompare is a modest tool that takes a library of known sequence-structure pairs, e.g. Andronescu et al. (2008), and predictions by different algorithms and produces tables for easy comparison of different programs. It was written to automate the rather tedious procedure of comparing and testing different programs. The library behind this tool can be of interest if you want to train folding algorithms and need a way to quickly ascertain training success.

::DEVELOPER

Ivo Hofacker

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

SSPcompare

:: MORE INFORMATION

Citation

Höner zu Siederdissen, Christian, Stephan H. Bernhart, Peter F. Stadler, and Ivo L. Hofacker. 2011.
A Folding Algorithm for Extended RNA Secondary Structures.
Bioinformatics 27: 129–36.

RNAwolf 0.3.2 / MC-Fold-DP – RNA Secondary Structure Prediction.

RNAwolf 0.3.2 / MC-Fold-DP

:: DESCRIPTION

RNAwolf and MC-Fold-DP are two programs (rather, collections of a library and several programs, each) that deal with RNA secondary structure prediction.

::DEVELOPER

Ivo Hofacker

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

RNAwolf 0.3.2 / MC-Fold-DP

:: MORE INFORMATION

Citation

Höner zu Siederdissen, Christian, Stephan H. Bernhart, Peter F. Stadler, and Ivo L. Hofacker. 2011.
A Folding Algorithm for Extended RNA Secondary Structures.
Bioinformatics 27: 129–36.

CMCompare 0.0.1 – Discriminatory Power of RNA Family Models

CMCompare 0.0.1

:: DESCRIPTION

The CMCompare program takes two Infernal covariance models and calculates the Link sequence and its Link score. The Link sequence is the sequence scored by both models highest at the same time. Two models with a high Link score are not well separated from each other.

::DEVELOPER

Ivo Hofacker

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

CMCompare

:: MORE INFORMATION

Citation

Discriminatory power of RNA family models
Höner zu Siederdissen, Christian and Hofacker, Ivo L.
Bioinformatics, 2010, 26, 453-459

expected5to3distance – Compute Expected Distance between Terminal Nucleotides of RNA

expected5to3distance

:: DESCRIPTION

expected5to3distance is a web server that computes the expected distance between the 5′ and 3′ ends of the Boltzmann ensemble of all secondary structures for a given RNA sequence

:: DEVELOPER

Clote Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Linux / MacOsX
Python / C COmpiler

:: DOWNLOAD

expected5to3distance

:: MORE INFORMATION

Citation

Expected distance between terminal nucleotides of RNA secondary structures
P. Clote, Y. Ponty, J.-M. Steyaert
Journal of Mathematical Biology (2012).

Dishuffle – RNA Dinucleotide Shuffle

Dishuffle

:: DESCRIPTION

Dishuffle is a web interface to a local implementation of the Altschul-Erikson dinucleotide shuffle algorithm, described in “Significance of nucleotide sequence alignments: A method for random sequence permutation that preserves dinucleotide and codon usage”

:: DEVELOPER

Clote Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Linux / MacOsX
Python

:: DOWNLOAD

Dishuffle

:: MORE INFORMATION

Citation

RNA. 2005 May;11(5):578-91.
Structural RNA has lower folding energy than random RNA of the same dinucleotide frequency.
Clote P, Ferré F, Kranakis E, Krizanc D.

RNAmotifs 3 – Predict a motif for your own set of RNAs

RNAmotifs 3

:: DESCRIPTION

RNAmotifs allows you to predict a structural motif common to a set of RNA sequences. The resulting motifs includes information on both RNA sequence and structure. Motifs are described both graphically and by a data file containing information on the underlying probabilistic model.

::DEVELOPER

Segal Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

RNAmotifs

:: MORE INFORMATION

Citation

Rabani et. al,
Computational prediction of RNA structural motifs involved in post transcriptional regulatory processes,
Proc Natl Acad Sci U S A., September 2008

RD – Statistical Estimation of Isoform Expression Levels using RNA-Seq Based on the Modeling of RNA Degradation

RD

:: DESCRIPTION

RD is intended to implement a program for statistical estimation of isoform expression levels using RNA-Seq based on the modeling of RNA degradation.

::DEVELOPER

Fengzhu Sun

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Linux / MacOsX
perl
R Package

:: DOWNLOAD

:: MORE INFORMATION

Citation

Wan L, Yan XT, Chen T and Sun FZ (2011)
RD: A Program for Statistical Estimation of Isoform Expression Levels using RNA-Seq Based on the Modeling of RNA Degradation
submitted.

RNACluster 1.0 – RNA Secondary Structure Comparison and Clustering

RNACluster 1.0

:: DESCRIPTION

RNACluster is an integrated computational software which implements 6 common structure distances to measure the (dis)similarity of RNA secondary structures including base pair distance, mountain distance, morphological distance, tree edit distance, string edit distance and our in-house structure matrix distance, and one effective cluster approach for the ensemble clustering using a minimum spanning tree (MST) based algorithm. RNACluster can be used to study the characteristics of RNA secondary structures, RNA structure conformational switches, RNA conformational energy landscapes and RNA secondary structure prediction based on the clustering of structure ensemble.

::DEVELOPER

Qi Liu

:: REQUIREMENTS

Linux/Windows

:: DOWNLOAD

RNACluster

:: MORE INFORMATION

Citation

Liu Q, Olman V, Liu H, Ye X, Qiu S, Xu Y.
RNACluster: An integrated tool for RNA secondary structure comparison and clustering.
J Comput Chem. 2008 Jul 15;29(9):1517-26.

Randfold 2.0 – RNA Minimum Free Energy of Folding Randomization Test

Randfold 2.0

:: DESCRIPTION

Randfold compute the probability that, for a given RNA sequence, the Minimum Free Energy (MFE) of the secondary structure is different from a distribution of MFE computed with random sequences.

:: DEVELOPER

Bioinformatics & Systems Biology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

Randfold

:: MORE INFORMATION

Citation:

Bonnet, E., * Wuyts, J., Rouzé, P., Van de Peer, Y. (2004)
Evidence that microRNA precursors, unlike other non-coding RNAs, have lower folding free energies than random sequences.
Bioinformatics 20, 2911-7