MXSCARNA (Multiplex Stem Candidate Aligner for RNAs) is a multiple alignment tool for RNA sequences using progressive alignment based on pairwise structural alignment algorithm of SCARNA. This software is fast enough for large scale analyses, while the accuracies of the alignments are better than or comparable with the existing algorithms which are computationally much more expensive in time and memory.


Murlet is a practical alignment tool for structural RNA sequences. It is based on the Sankoff algorithm and uses an efficient scoring system that considerably reduces the time and space requirements without degrading alignment quality.


RNAmine is a software tool to extract the structural motifs from a set of RNA sequences using a graph mining technique. Developed by Mizuho Information & Research Institute.


SCARNA is an alignment tool for a pair of RNA sequences based on the predicted common secondary structure.


PHMMTS (Pair Hidden Markov Models on Tree Structures) aligns a sequence of unknown secondary structure to a sequence of known secondary structure.


PSTAG (Pair Stochastic Tree Adjoining Grammars) for RNA sequences including pseudoknotted structures.


Rfold computes local base pairing probabilities for long DNA sequences.

Stem Kernels

The stem kernel is a kernel function for structural RNAs to measure a kind of similarity between a pair of RNA sequences from the viewpoint of secondary structures.


CentroidFold based on a generalized centroid estimator is one of the most accurate tools for predicting RNA secondary structures. See the original paper for the details of the algorithm.


Accurate (common) secondary structure prediction for aligned RNA sequences


RNA Secondary Structure Prediction using Homologous Sequences


CentroidAlign is an accurate and fast aligner for multiple RNA sequences, based on maximizing the expected sum-of-pair score (SPS)


miRRim is a method for detecting miRNA foldbacks based on hidden Markov model (HMM). In this method, the evolutionary and secondary structural features of a miRNA region is represented by a sequence of multidimensional vectors. HMMs that generate a sequence of continuous values are used to model the feature vector sequences.


SCARNA_LM (SCARNA Local Multiple) is a local multiple aligner for RNA sequences. It is based on a discriminative pairwise alignment model which incorporates secondary structure features as base pairing probability calculrated by Rfold, and uses an efficient local multiple alignment construction procedure proposed by Phuong et al for local multiple alignment of protein sequences. As postprocessing, it calcurates global multiple alignments via MXSCARNA.


A non-parametric Bayesian approach for predicting RNA secondary structures


fast and accurate prediction of RNA-RNA interaction using integer programming


RNA pseudoknot prediction based on maximizing expected accuracy


A tool for genome-scale computation of structural accessibility of RNA transcripts.


Fdur computes sufficient statistics of phylogenetic tree models


computes entropy, mean energy, and variation of energy from the Boltzmann distribution of RNA secondary structures


Rchange computes energy changes of RNA secondary structures after base mutations.


Simultaneous aligning and folding of RNA sequences by dual decomposition


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